协调数
协调球
化学
金属
蛋白质数据库
结晶学
蛋白质数据库
配位复合体
金属蛋白
晶体结构
水溶液中的金属离子
氨基酸
配位几何学
蛋白质结构
离子
立体化学
分子
生物化学
氢键
有机化学
作者
Ivan Dokmanić,Mile Šikić,Sanja Tomić
出处
期刊:Acta Crystallographica Section D-biological Crystallography
[International Union of Crystallography]
日期:2008-02-20
卷期号:64 (3): 257-263
被引量:189
标识
DOI:10.1107/s090744490706595x
摘要
Metal ions are constituents of many metalloproteins, in which they have either catalytic (metalloenzymes) or structural functions. In this work, the characteristics of various metals were studied (Cu, Zn, Mg, Mn, Fe, Co, Ni, Cd and Ca in proteins with known crystal structure) as well as the specificity of their environments. The analysis was performed on two data sets: the set of protein structures in the Protein Data Bank (PDB) determined with resolution <1.5 Å and the set of nonredundant protein structures from the PDB. The former was used to determine the distances between each metal ion and its electron donors and the latter was used to assess the preferred coordination numbers and common combinations of amino-acid residues in the neighbourhood of each metal. Although the metal ions considered predominantly had a valence of two, their preferred coordination number and the type of amino-acid residues that participate in the coordination differed significantly from one metal ion to the next. This study concentrates on finding the specificities of a metal-ion environment, namely the distribution of coordination numbers and the amino-acid residue types that frequently take part in coordination. Furthermore, the correlation between the coordination number and the occurrence of certain amino-acid residues (quartets and triplets) in a metal-ion coordination sphere was analysed. The results obtained are of particular value for the identification and modelling of metal-binding sites in protein structures derived by homology modelling. Knowledge of the geometry and characteristics of the metal-binding sites in metalloproteins of known function can help to more closely determine the biological activity of proteins of unknown function and to aid in design of proteins with specific affinity for certain metals.
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