Rulísek L, Vondrásek J
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
J Inorg Biochem. 1998 Sep;71(3-4):115-27. doi: 10.1016/s0162-0134(98)10042-9.
In order to determine preferred coordination geometries of six divalent cations (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+), two sources of experimental data were exploited: Protein Data Bank and Cambridge Structural Database. Metal-binding sites of approximately 100 metalloproteins and 3000 smaller transition metal complexes were analyzed and classified. The correlation between the geometries of small-molecule crystal structures and the metal-binding sites in metalloproteins was investigated. The abundance of amino acid residues participating in coordination metal-protein bonds of metalloproteins was evaluated. From the performed analysis it follows that the octahedral arrangement is preferred by Co2+ and Ni2+, tetrahedral by Zn2+, square planar by Cu2+, and linear by Hg2+. Cadmium (II) cation tends to bind in both tetrahedral and octahedral arrangements and single coordination geometry cannot be unambiguously ascribed to it.
为了确定六种二价阳离子（Co2+、Ni2+、Cu2+、Zn2+、Cd2+和Hg2+）的优选配位几何结构，利用了两种实验数据来源：蛋白质数据库和剑桥结构数据库。分析并分类了约100种金属蛋白和3000种较小的过渡金属配合物的金属结合位点。研究了小分子晶体结构的几何结构与金属蛋白中金属结合位点之间的相关性。评估了参与金属蛋白配位金属-蛋白质键的氨基酸残基的丰度。从所进行的分析可以得出，Co2+和Ni2+优选八面体排列，Zn2+优选四面体排列，Cu2+优选平面正方形排列，Hg2+优选线性排列。镉（II）阳离子倾向于以四面体和八面体两种排列方式结合，无法明确地将单一配位几何结构归因于它。
