Harding Marjorie M
Institute of Structural and Molecular Biology, Michael Swann Building, University of Edinburgh, Edinburgh EH9 3JR, Scotland.
Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):678-82. doi: 10.1107/S0907444906014594. Epub 2006 May 12.
A new analysis has been made of distances around metal sites in protein structures in the Protein Data Bank determined with resolution < or =1.25 A and equivalent distances have been extracted from the Cambridge Structural Database. They are for the metals Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn and the donor atoms O of water, O of Asp and Glu, O of the main-chain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of 'target distances' previously given. As well as small changes in many distances and a large improvement for Mg-O(carboxylate), the table includes an indication of how reliable each prediction may be. Special attention was given to carboxylate interactions. When the carboxylate group is monodentate, the M-O(carboxylate) distance is well defined, but for bidentate carboxylate groups a wide range of distances is allowable; when the metal is Co, Cu or Zn the M-O(1) and M-O(2) distances are clearly inversely correlated; for the more purely electrostatic interactions involving Na, K and Ca there is a wider scatter of distances and little correlation.
对蛋白质数据库中分辨率≤1.25埃的蛋白质结构中金属位点周围的距离进行了新的分析，并从剑桥结构数据库中提取了等效距离。这些距离涉及的金属有钠、镁、钾、钙、锰、铁、钴、铜、锌，供体原子包括水分子中的氧、天冬氨酸和谷氨酸中的氧、主链羰基中的氧、组氨酸中的氮以及半胱氨酸中的硫。建议对之前给出的“目标距离”表格进行一些修订。除了许多距离有微小变化以及镁-氧（羧酸盐）距离有较大改善外，该表格还给出了每个预测可靠性的指示。特别关注了羧酸盐相互作用。当羧酸盐基团为单齿时，金属-氧（羧酸盐）距离定义明确，但对于双齿羧酸盐基团，允许有很宽的距离范围；当金属为钴、铜或锌时，金属-氧（1）和金属-氧（2）距离明显呈负相关；对于涉及钠、钾和钙的更纯粹的静电相互作用，距离的分散性更大且相关性很小。
