Journal articles: 'Metal binding sites'

1

Tainer, John A., Victoria A. Roberts, and Elizabeth D. Getzoff. "Protein metal-binding sites." Current Biology 2, no. 10 (October 1992): 552. http://dx.doi.org/10.1016/0960-9822(92)90035-9.

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Tainer, John A., Victoria A. Roberts, and Elizabeth D. Getzoff. "Protein metal-binding sites." Current Opinion in Biotechnology 3, no. 4 (August 1992): 378–87. http://dx.doi.org/10.1016/0958-1669(92)90166-g.

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3

Tainer, John A., Victoria A. Roberts, and Elizabeth D. Getzoff. "Metal-binding sites in proteins." Current Opinion in Biotechnology 2, no. 4 (August 1991): 582–91. http://dx.doi.org/10.1016/0958-1669(91)90084-i.

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4

Sharma, Ashok, Sudeep Roy, Kumar Parijat Tripathi, Pratibha Roy, Manoj Mishra, Feroz Khan, and Abha Meena. "Predicted metal binding sites for phytoremediation." Bioinformation 4, no. 2 (September 5, 2009): 66–70. http://dx.doi.org/10.6026/97320630004066.

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Lu, Yi, and Joan S. Valentine. "Engineering metal-binding sites in proteins." Current Opinion in Structural Biology 7, no. 4 (August 1997): 495–500. http://dx.doi.org/10.1016/s0959-440x(97)80112-1.

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6

Regan, Lynne. "Protein design: novel metal-binding sites." Trends in Biochemical Sciences 20, no. 7 (July 1995): 280–85. http://dx.doi.org/10.1016/s0968-0004(00)89044-1.

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7

Illi, Sarah, Johanna Schulten, and Peter Klüfers. "Metal-binding Sites ofN-Acetylneuraminic Acid." Zeitschrift für anorganische und allgemeine Chemie 639, no. 1 (October 30, 2012): 77–83. http://dx.doi.org/10.1002/zaac.201200415.

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Kökçam-Demir, Ülkü, Anna Goldman, Leili Esrafili, Maniya Gharib, Ali Morsali, Oliver Weingart, and Christoph Janiak. "Coordinatively unsaturated metal sites (open metal sites) in metal–organic frameworks: design and applications." Chemical Society Reviews 49, no. 9 (2020): 2751–98. http://dx.doi.org/10.1039/c9cs00609e.

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The defined synthesis of OMS in MOFs is the basis for targeted functionalization through grafting, the coordination of weakly binding species and increased (supramolecular) interactions with guest molecules.

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Gilg, Kathrin, Tobias Mayer, Natascha Ghaschghaie, and Peter Klüfers. "The metal-binding sites of glycose phosphates." Dalton Transactions, no. 38 (2009): 7934. http://dx.doi.org/10.1039/b909431h.

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10

Passerini, A., M. Lippi, and P. Frasconi. "Predicting Metal-Binding Sites from Protein Sequence." IEEE/ACM Transactions on Computational Biology and Bioinformatics 9, no. 1 (January 2012): 203–13. http://dx.doi.org/10.1109/tcbb.2011.94.

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11

Martin, R. Bruce. "Nucleoside sites for transition metal ion binding." Accounts of Chemical Research 18, no. 2 (February 1985): 32–38. http://dx.doi.org/10.1021/ar00110a001.

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12

Marcoux, Pierre R., Bernold Hasenknopf, Jacqueline Vaissermann, and Pierre Gouzerh. "Developing Remote Metal Binding Sites in Heteropolymolybdates." European Journal of Inorganic Chemistry 2003, no. 13 (July 2003): 2406–12. http://dx.doi.org/10.1002/ejic.200200677.

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13

Svensson, Lars Anders, Lars Thim, Ole Hvilsted Olsen, and Else Marie Nicolaisen. "Evaluation of the metal binding sites in a recombinant coagulation factor VIII identifies two sites with unique metal binding properties." Biological Chemistry 394, no. 6 (June 1, 2013): 761–65. http://dx.doi.org/10.1515/hsz-2012-0298.

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Abstract Coagulation factor VIII is a glycosylated, non-covalent heterodimer consisting of a heavy chain (A1-A2-B domains) and a light chain (A3-C1-C2 domains). The association of the chains, and the stability and function of the dimer depend on the presence of metal ions. We applied X-ray fluorescence, X-ray crystallographic structure determination with anomalous signals at different wavelengths, and colorimetric measurements to evaluate the metal binding sites in a recombinant factor VIII molecule, turoctocog alfa. We identified a metal binding site in domain A3 dominated by Cu+ binding and a site in domain A1 dominated by Zn2+ binding.

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Zheng, Heping, David R. Cooper, Przemyslaw J. Porebski, Ivan G. Shabalin, Katarzyna B. Handing, and Wladek Minor. "CheckMyMetal: a macromolecular metal-binding validation tool." Acta Crystallographica Section D Structural Biology 73, no. 3 (February 22, 2017): 223–33. http://dx.doi.org/10.1107/s2059798317001061.

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Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites.CheckMyMetal(CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. TheCMMserver can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples showCMMusers (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.

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15

Veenstra, Timothy D., Myron D. Gross, Willi Hunziker, and Rajiv Kumar. "Identification of Metal-binding Sites in Rat Brain Calcium-binding Protein." Journal of Biological Chemistry 270, no. 51 (December 22, 1995): 30353–58. http://dx.doi.org/10.1074/jbc.270.51.30353.

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16

Regan, L. "The Design of Metal-Binding Sites in Proteins." Annual Review of Biophysics and Biomolecular Structure 22, no. 1 (June 1993): 257–81. http://dx.doi.org/10.1146/annurev.bb.22.060193.001353.

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17

Yuriev, Elizabeth, and John D. Orbell. "Steric Parameters for Metal Binding Sites on Nucleobases." Inorganic Chemistry 35, no. 26 (January 1996): 7914–15. http://dx.doi.org/10.1021/ic9610896.

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18

Ariki, M., and J. K. Lanyi. "Characterization of metal ion-binding sites in bacteriorhodopsin." Journal of Biological Chemistry 261, no. 18 (June 1986): 8167–74. http://dx.doi.org/10.1016/s0021-9258(19)83892-9.

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19

Shimakoshi, Hisashi, Hiroki Takemoto, Isao Aritome, and Yoshio Hisaeda. "New macrocyclic ligands having discrete metal binding sites." Tetrahedron Letters 43, no. 27 (July 2002): 4809–12. http://dx.doi.org/10.1016/s0040-4039(02)00923-1.

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20

Beer, Paul D., Christopher J. Jones, Jon A. McCleverty, and Sithy S. Salam. "Redox responsive metal complexes containing cation binding sites." Journal of Inclusion Phenomena 5, no. 4 (August 1987): 521–24. http://dx.doi.org/10.1007/bf00664111.

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21

Richmond, Todd A., Terry T. Takahashi, Riti Shimkhada, and Jennifer Bernsdorf. "Engineered Metal Binding Sites on Green Fluorescence Protein." Biochemical and Biophysical Research Communications 268, no. 2 (February 2000): 462–65. http://dx.doi.org/10.1006/bbrc.1999.1244.

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22

Qu, Jing, Sheng S. Yin, and Han Wang. "Prediction of Metal Ion Binding Sites of Transmembrane Proteins." Computational and Mathematical Methods in Medicine 2021 (October 22, 2021): 1–11. http://dx.doi.org/10.1155/2021/2327832.

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The metal ion binding of transmembrane proteins (TMPs) plays a fundamental role in biological processes, pharmaceutics, and medicine, but it is hard to extract enough TMP structures in experimental techniques to discover their binding mechanism comprehensively. To predict the metal ion binding sites for TMPs on a large scale, we present a simple and effective two-stage prediction method TMP-MIBS, to identify the corresponding binding residues using TMP sequences. At present, there is no specific research on the metal ion binding prediction of TMPs. Thereby, we compared our model with the published tools which do not distinguish TMPs from water-soluble proteins. The results in the independent verification dataset show that TMP-MIBS has superior performance. This paper explores the interaction mechanism between TMPs and metal ions, which is helpful to understand the structure and function of TMPs and is of great significance to further construct transport mechanisms and identify potential drug targets.

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23

Lecerof, David, Michel N. Fodje, Román Alvarez León, Ulf Olsson, Andreas Hansson, Emma Sigfridsson, Ulf Ryde, Mats Hansson, and Salam Al-Karadaghi. "Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites." JBIC Journal of Biological Inorganic Chemistry 8, no. 4 (January 18, 2003): 452–58. http://dx.doi.org/10.1007/s00775-002-0436-1.

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24

Acharya, Shveta, and Arun Kumar Sharma. "The Thermodynamic and pH Metric Binding Studies of Cu+2 Ions with Egg Protein by Spectrometric and Diffusion Current Techniques." Zeitschrift für Physikalische Chemie 234, no. 3 (March 26, 2020): 441–60. http://dx.doi.org/10.1515/zpch-2018-1320.

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AbstractTransition metals have unique efficacy in catalyzing various industrial reactions and also in living system, the redox reaction and redox changes in the metal ions catalyzed valence changes in the substrate molecule. The survey of the existing literature revealed that the binding of Molybdenum, Vanadium, Zinc, Cadmium, Copper, Nickel and Cobalt with the protein is well known but no binding studies of copper metal with egg protein are reported. With a view to extend the existing knowledge of ecological nature of metal-protein system, it was thought of interest to investigate the properties of metal-protein mixture. Investigations on the aspects of these binding problems were planned and their bindings constants have been determined using suitable physico-chemical methods. The pH metric, diffusion current measurements, spectrophotometric methods have been used on the binding of copper ions with albumin. The effect of physico-chemical factors on interaction between divalent metal ion i.e. copper with albumin has been discussed. On the basis of observed results, it is found that the binding data were dependent on pH and temperature. From scatchard plots, the intrinsic association constants (k) and the number of binding sites (n) were calculated and found high at lower pH and temperatures. Therefore, a lower temperature and lower pH offered more sites in the protein molecule for interaction with copper (II) ions. The enthalpy (ΔH), entropy (ΔS) changes, free energy change (ΔG°) have been calculated.

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25

Groves, P., and M. Palczewska. "Cation binding properties of calretinin, an EF-hand calcium-binding protein." Acta Biochimica Polonica 48, no. 1 (March 31, 2001): 113–19. http://dx.doi.org/10.18388/abp.2001_5117.

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Calretinin (CR) is a neuronal EF-hand protein previously characterized as a calcium (micromolar affinity) binding protein. CR-containing neurons are spared in some neurodegenerative diseases, although it is as yet unconfirmed how CR plays an active role in this protection. Higher levels of some metal cations (e.g. copper and zinc) are associated with these diseases. At the same time, metals such as terbium (NMR and fluorescence) cadmium (NMR) and manganese (EPR) serve as useful calcium analogues in the study of EF-hand proteins. We survey the binding of the above-mentioned metal cations that might affect the structure and function of CR. Competitive 45Ca2+-overlay, competitive terbium fluorescence and intrinsic tryptophan fluorescence are used to detect the binding of metal cations to CR. Terbium and copper (half-maximal effect of 15 microM) bind to CR. Terbium has a similar or greater affinity for the calcium-binding sites of CR than calcium. Copper quenches the fluorescence of terbium-bound CR, and CR tryptophan residues and competes weakly for 45Ca2+-binding sites. Cadmium, magnesium, manganese and zinc bind less strongly (half-maximal effects above 0.1 mM). Therefore, only terbium appears to be a suitable analytical calcium analogue in further studies of CR. The principal conclusion of this work is that copper, in addition to calcium, might be a factor in the function of CR and a link between CR and neurodegenerative diseases.

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26

Dorner, S., and A. Barta. "Probing Ribosome Structure by Europium-Induced RNA Cleavage." Biological Chemistry 380, no. 2 (February 1, 1999): 243–51. http://dx.doi.org/10.1515/bc.1999.032.

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AbstractDivalent metal ions are absolutely required for the structure and catalytic activities of ribosomes. They are partly coordinated to highly structured RNA, which therefore possesses high-affinity metal ion binding pockets. As metalion induced RNA cleavages are useful for characterising metal ion binding sites and RNA structures, we analysed europium (Eu3+) induced specific cleavages in both 16S and 23S rRNA ofE. coli. The cleavage sites were identified by primer extension and compared to those previously identified for calcium, lead, magnesium, and manganese ions. Several Eu3+cleavage sites, mostly those at which a general metal ion binding site had been already identified, were identical to previously described divalent metal ions. Overall, the Eu3+cleavages are most similar to the Ca2+cleavage pattern, probably due to a similar ion radius. Interestingly, several cleavage sites which were specific for Eu3+were located in regions implicated in the binding of tRNA and antibiotics. The binding of erythromycin and chloramphenicol, but not tetracycline and streptomycin, significantly reduced Eu3+cleavage efficiencies in the peptidyl transferase center. The identification of specific Eu3+binding sites near the active sites on the ribosome will allow to use the fluorescent properties of europium for probing the environment of metal ion binding pockets at the ribosome's active center.

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27

Nauroozi, Djawed, Benjamin Wurster, and Rüdiger Faust. "Cross-π-conjugated enediyne with multitopic metal binding sites." RSC Advances 10, no. 63 (2020): 38612–16. http://dx.doi.org/10.1039/d0ra06320g.

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28

Perera, Rukshan, Syed Ashraf, and Anja Mueller. "The binding of metal ions to molecularly-imprinted polymers." Water Science and Technology 75, no. 7 (January 23, 2017): 1643–50. http://dx.doi.org/10.2166/wst.2017.036.

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Imprinting polymerization is a flexible method to make resins specific for different compounds. Imprinting polymerization involves the polymerization of the resin in the presence of a template, here cadmium ions or arsenate. The template is then removed by washing, leaving specific binding sites in the resin. In water treatment, the removal of toxic metal ions is difficult due to the limited affinity of these ions to ion exchange resins. Imprinting polymerization of ion-exchange resins is used to develop resins with high capacity and some selectivity for cadmium ions or arsenate for water treatment that still function as general ion-exchange resins. A minimum binding capacity of 325 meq/g was achieved for cadmium ions. Competition experiments elucidate the type of bonds present in the imprinting complex. The capacity and bond types for the cadmium ions and arsenate were contrasted. In the case of cadmium, metal-ligand bonds provide significant specificity of binding, although significant binding also occurs to non-specific surface sites. Arsenate ions are larger than cadmium ions and can only bind via ionic and hydrogen bonds, which are weaker than metal-ligand bonds. This results in lower specificity for arsenate. Additionally, diffusion into the resin is a limiting factor due to the larger size of the arsenate ion. These data elucidate the bonds formed between metal ions and the imprinting sites as well as other parameters that increase the capacity for heavy metals and arsenate.

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29

Vogel, Manja, Sabine Matys, Falk Lehmann, Björn Drobot, Tobias Günther, Katrin Pollmann, and Johannes Raff. "Use of Specific Metal Binding of Self-Assembling S-Layer Proteins for Metal Bioremediation and Recycling." Solid State Phenomena 262 (August 2017): 389–93. http://dx.doi.org/10.4028/www.scientific.net/ssp.262.389.

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Most bacteria and all archaea possess as outermost cell envelope so called surface-layers (S-layers). These layers were formed by self-assembling proteins having a number of habitat depending interesting intrinsic properties. As example, S-layers from bacterial isolates recovered from heavy metal contaminated environments have outstanding metal binding properties and are highly stable. Thus they selectively bind several metals with different affinity. For using S-layer proteins for metal bioremediation and recycling three aspects of the metal-interactions with S-layer proteins must be taken into account. First, S-layers possess different functionalities, e.g. carboxyl, phosphoryl groups, binding toxic metals and metalloids, like U(VI) and As(V), nonspecifically depending on pH. Second, precious metals like Au and Pd are likewise nonspecifically bound to functional groups, but presumably covalently, making the binding irreversible. Third, intrinsic specifically bound metals, e.g. Ca2+, are needed for native protein folding, self-assembly, and the formation of highly-ordered lattices. Their binding sites also allow selective binding of chemical-equal elements including the trivalent rare earth elements, possessing comparable ionic radii. Thus this study combines older and recently generated results regarding the metal dependent binding behavior of the S-layer proteins. It enables the development of biohybrid materials for the separation, removal or recovery of strategic relevant metals from natural occurring or industrial waste waters using pH-value as regulating parameter for selective metal binding and also conceivably release.

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30

Garg, Aditi, and Debnath Pal. "Inferring metal binding sites in flexible regions of proteins." Proteins: Structure, Function, and Bioinformatics 89, no. 9 (April 26, 2021): 1125–33. http://dx.doi.org/10.1002/prot.26085.

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31

Vang, Janus, Yulia Pustovalova, Dmitry M. Korzhnev, Oksana Gorbatyuk, Camille Keeler, Michael E. Hodsdon, and Jeffrey C. Hoch. "Architecture of the two metal-binding sites in prolactin." Biophysical Journal 121, no. 7 (April 2022): 1312–21. http://dx.doi.org/10.1016/j.bpj.2022.02.024.

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32

Zheng, Huiling, Hao Li, Long Luo, Zhen Zhao, and Graeme Henkelman. "Factors that influence hydrogen binding at metal-atop sites." Journal of Chemical Physics 155, no. 2 (July 14, 2021): 024703. http://dx.doi.org/10.1063/5.0056774.

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33

Ushiyama, Masato, Yoji Katayama, and Takeshi Yamamura. "Histidine Containing Porphyrins Directed for Two Metal Binding Sites." Chemistry Letters 24, no. 5 (May 1995): 395–96. http://dx.doi.org/10.1246/cl.1995.395.

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34

Badarau, Adriana, Susan J. Firbank, Andrew A. McCarthy, Mark J. Banfield, and Christopher Dennison. "Visualizing the Metal-Binding Versatility of Copper Trafficking Sites,." Biochemistry 49, no. 36 (September 14, 2010): 7798–810. http://dx.doi.org/10.1021/bi101064w.

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35

MATTHEWS, J., F. LOUGHLIN, and J. MACKAY. "Designed metal-binding sites in biomolecular and bioinorganic interactions." Current Opinion in Structural Biology 18, no. 4 (August 2008): 484–90. http://dx.doi.org/10.1016/j.sbi.2008.04.009.

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36

Kankare, Jussi, Tiina Salminen, Reijo Lahti, Barry S. Cooperman, Alexander A. Baykov, and Adrian Goldman. "Crystallographic Identification of Metal-Binding Sites inEscherichia coliInorganic Pyrophosphatase†,‡." Biochemistry 35, no. 15 (January 1996): 4670–77. http://dx.doi.org/10.1021/bi952637e.

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37

Dunbar, Robert C., Nicolas C. Polfer, Giel Berden, and Jos Oomens. "Metal ion binding to peptides: Oxygen or nitrogen sites?" International Journal of Mass Spectrometry 330-332 (December 2012): 71–77. http://dx.doi.org/10.1016/j.ijms.2012.10.006.

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38

Papadakos, Grigorios A., Horacio Nastri, Paul Riggs, and Cynthia M. Dupureur. "Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis." JBIC Journal of Biological Inorganic Chemistry 12, no. 4 (February 17, 2007): 557–69. http://dx.doi.org/10.1007/s00775-007-0209-y.

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39

Miller, Yifat, Buyong Ma, and Ruth Nussinov. "Metal binding sites in amyloid oligomers: Complexes and mechanisms." Coordination Chemistry Reviews 256, no. 19-20 (October 2012): 2245–52. http://dx.doi.org/10.1016/j.ccr.2011.12.022.

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40

Ghaschghaie, Natascha, Thomas Hoffmann, Martin Steinborn, and Peter Klüfers. "The tridentate metal-binding sites of the common glycoses." Dalton Transactions 39, no. 23 (2010): 5535. http://dx.doi.org/10.1039/b925537k.

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41

Ordóñez, Efrén, Saravanamuthu Thiyagarajan, Jeremy D. Cook, Timothy L. Stemmler, José A. Gil, Luís M. Mateos, and Barry P. Rosen. "Evolution of Metal(loid) Binding Sites in Transcriptional Regulators." Journal of Biological Chemistry 283, no. 37 (June 30, 2008): 25706–14. http://dx.doi.org/10.1074/jbc.m803209200.

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42

Denesyuk, Alexander I., Sergei E. Permyakov, Mark S. Johnson, Eugene A. Permyakov, and Konstantin Denessiouk. "Building kit for metal cation binding sites in proteins." Biochemical and Biophysical Research Communications 494, no. 1-2 (December 2017): 311–17. http://dx.doi.org/10.1016/j.bbrc.2017.10.034.

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43

Wineman-Fisher, Vered, and Yifat Miller. "Insight into the Metal Binding Sites in Amylin Aggregates." Biophysical Journal 108, no. 2 (January 2015): 524a. http://dx.doi.org/10.1016/j.bpj.2014.11.2873.

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Sobolev, Vladimir, and Marvin Edelman. "Web Tools for Predicting Metal Binding Sites in Proteins." Israel Journal of Chemistry 53, no. 3-4 (April 2013): 166–72. http://dx.doi.org/10.1002/ijch.201200084.

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Nell, Ryan M., and Jeremy B. Fein. "Influence of sulfhydryl sites on metal binding by bacteria." Geochimica et Cosmochimica Acta 199 (February 2017): 210–21. http://dx.doi.org/10.1016/j.gca.2016.11.039.

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Clarke, Neil D., and Shao-Min Yuan. "Metal search: A computer program that helps design tetrahedral metal-binding sites." Proteins: Structure, Function, and Genetics 23, no. 2 (October 1995): 256–63. http://dx.doi.org/10.1002/prot.340230214.

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47

Radka, Christopher D., Lawrence J. DeLucas, Landon S. Wilson, Matthew B. Lawrenz, Robert D. Perry, and Stephen G. Aller. "Crystal structure ofYersinia pestisvirulence factor YfeA reveals two polyspecific metal-binding sites." Acta Crystallographica Section D Structural Biology 73, no. 7 (June 30, 2017): 557–72. http://dx.doi.org/10.1107/s2059798317006349.

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Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. InYersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.

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Zheng, Heping, Mahendra Chordia, David Cooper, Ivan Shabalin, Maksymilian Chruszcz, Peter Müller, George Sheldrick, and Wladek Minor. "Check your metal - not every density blob is a water molecule." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1483. http://dx.doi.org/10.1107/s2053273314085167.

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Metals play vital roles in both the mechanism and architecture of biological macromolecules, and are the most frequently encountered ligands (i.e. non-solvent heterogeneous chemical atoms) in the determination of macromolecular crystal structures. However, metal coordinating environments in protein structures are not always easy to check in routine validation procedures, resulting in an abundance of misidentified and/or suboptimally modeled metal ions in the Protein Data Bank (PDB). We present a solution to identify these problems in three distinct yet related aspects: (1) coordination chemistry; (2) agreement of experimental B-factors and occupancy; and (3) the composition and motif of the metal binding environment. Due to additional strain introduced by macromolecular backbones, the patterns of coordination of metal binding sites in metal-containing macromolecules are more complex and diverse than those found in inorganic or organometallic chemistry. These complications make a comprehensive library of "permitted" coordination chemistry in protein structures less feasible, and the usage of global parameters such as the bond valence method more practical, in the determination and validation of metal binding environments. Although they are relatively infrequent, there are also cases where the experimental B-factor or occupancy of a metal ion suggests careful examination. We have developed a web-based tool called CheckMyMetal [1](http://csgid.org/csgid/metal_sites/) for the quick validation of metal binding sites. Moreover, the acquired knowledge of the composition and spatial arrangement (motif) of the coordinating atoms around the metal ion may also help in the modeling of metal binding sites in macromolecular structures. All of the studies described herein were performed using the NEIGHBORHOOD SQL database [2], which connects information about all modeled non-solvent heterogeneous chemical motifs in PDB structure by vectors describing all contacts to neighboring residues and atoms. NEIGHBORHOOD has broad applications for the validation and data mining of ligand binding environments in the PDB.

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49

Ye, Jun, Ashoka Kandegedara, Philip Martin, and Barry P. Rosen. "Crystal Structure of the Staphylococcus aureus pI258 CadC Cd(II)/Pb(II)/Zn(II)-Responsive Repressor." Journal of Bacteriology 187, no. 12 (June 15, 2005): 4214–21. http://dx.doi.org/10.1128/jb.187.12.4214-4221.2005.

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ABSTRACT The Staphylococcus aureus plasmid pI258 cadCA operon encodes a P-type ATPase, CadA, that confers resistance to the heavy metals Cd(II), Zn(II), and Pb(II). Expression of this heavy-metal efflux pump is regulated by CadC, a homodimeric repressor that dissociates from the cad operator/promoter upon binding of Cd(II), Pb(II), or Zn(II). CadC is a member of the ArsR/SmtB family of metalloregulatory proteins. Here we report the X-ray crystal structure of CadC at 1.9 Å resolution. The dimensions of the protein dimer are approximately 30 Å by 40 Å by 70 Å. Each monomer contains six α-helices and a three-stranded β-sheet. Helices 4 and 5 form a classic helix-turn-helix motif that is the putative DNA binding region. The α1 helix of one monomer crosses the dimer to approach the α4 helix of the other monomer, consistent with the previous proposal that these two regulatory metal binding sites for the inducer cadmium or lead are each formed by Cys-7 and Cys-11 from the N terminus of one monomer and Cys-58 and Cys-60 of the other monomer. Two nonregulatory metal binding sites containing zinc are formed between the two antiparallel α6 helices at the dimerization interface. This is the first reported three-dimensional structure of a member of the ArsR/SmtB family with regulatory metal binding sites at the DNA binding domain and the first structure of a transcription repressor that responds to the heavy metals Cd(II) and Pb(II).

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Thomason, J. W., W. Susetyo, and L. A. Carreira. "Fluorescence Studies of Metal-Humic Complexes with the Use of Lanthanide Ion Probe Spectroscopy." Applied Spectroscopy 50, no. 3 (March 1996): 401–8. http://dx.doi.org/10.1366/0003702963906203.

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The acidic functional groups of humic materials are an abundant source of metal binding sites in the natural environment. Studies of metal binding to humics are of great environmental interest because the biological and physicochemical properties of metals are often changed dramatically as a result of complexation with humics. In order to understand how these heterogeneous organic macromolecules bind metals with such a large range of binding energies, lanthanide ion probe spectroscopy (LIPS) has been used to study changes in the fluorescence lifetime of the europium probe metal as it binds to these substances. A method developed by Horrocks and Sudnick for the determination of the number of water molecules bound to Eu3+ was used to calculate the coordination number of humic-bound Eu3+ from the fluorescence data. The peak shift of the Eu3+ hypersensitive emission band (616 nm) was used to calculate the change in charge of the complex. Equations based on Horrocks and Sudnick's method were also developed to calculate the distribution of metal associated with the different types of binding sites on humic substances by computer modeling of the fluorescence lifetime data.

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Journal articles on the topic 'Metal binding sites'

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