The geometry of metal-ligand interactions relevant to proteins
The geometry of metal-ligand interactions relevant to proteins
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DOI：
10.1107/s0907444999007374
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发表时间：
1999-08-01
期刊：
影响因子：
--
通讯作者：
Harding, MM
中科院分区：
文献类型：
--
作者：
Harding, MM
从剑桥结构数据库(CSD)中提取了可能与金属蛋白质的结构确定、结构精炼、评估或理解相关的几何数据。CSD包含了由X射线或中子衍射确定的小分子结构的结晶学数据，其准确性远远好于大多数当前的蛋白质结构测定。所选择的结构具有小于或等于0.065的晶体R因子，并且包含与作为蛋白质中常见的氨基酸侧链的类似物的配体相互作用的钙、镁、锰、铁、铜或锌；它们包括羧酸基、醇、酚酸盐、硫醇酸盐、咪唑基以及水分子。对于每一对，使用总共4500个类似的观测值，将平均金属-施主-原子距离、样品标准偏差和观测值范围列在表格中。在可行的情况下，给出具有不同配位数和/或氧化态的子集。还包括配体给体原子的键间夹角、羧酸基和咪唑基团相对于金属给体原子键的取向以及配体几何结构的一些其他方面。因此，例如，可以很容易地查找目标距离及其标准偏差，以验证金属蛋白结构或用于低分辨率数据的受限精化。
Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor less than or equal to 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal-donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using similar to 4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal-donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained refinement with low-resolution data.