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投稿者: Yuma Morimoto

亜鉛含有プロテインの亜鉛周りの構造についての論文。レゾリューションが悪いデータだと、平均距離が長めで出てくるらしい



Article

Zinc Coordination Spheres in Protein Structures

† University of Eastern Finland, Department of Chemistry, P.O. Box 111, FI-80101 Joensuu, Finland
‡ University of Tampere, Institute of Biomedical Technology, FI-33014, Tampere, Finland
Inorg. Chem., Article ASAP
DOI: 10.1021/ic401072d
Publication Date (Web): September 23, 2013
Copyright © 2013 American Chemical Society
*Tel.: +358-29-4453422. E-mail: janne.janis@uef.fi.

Abstract

Abstract Image
Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.
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雑誌会（200115）回答_藤田

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