Data mining of metal ion environments present in protein structures
Data mining of metal ion environments present in protein structures
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DOI：
10.1016/j.jinorgbio.2008.05.006
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发表时间：
2008-09-01
影响因子：
3.9
通讯作者：
Minor, Wladek
中科院分区：
文献类型：
--
作者：
Zheng, Heping;Chruszcz, Maksymilian;Minor, Wladek
金属-蛋白质相互作用的距离，配位数，B-因子（位移参数），和occupational的金属结合位点的蛋白质结构中确定的X射线晶体学和沉积在PDB的分析显示出许多不寻常的值和意想不到的相关性。通过测量金属离子结合位点中每个氨基酸的频率，确定每个残基对每种类型阳离子的正或负偏好。我们的方法可用于快速识别的金属结合的结构基序，不能单独的序列相似性的基础上确定。该分析将PDB中的高分辨率和中分辨率结构的数据与剑桥结构数据库（CSD）中的极高分辨率小分子结构的数据进行了比较。对于高分辨率的蛋白质结构，金属-蛋白质或金属-水相互作用距离的分布与CSD的数据相当一致，但对于中等分辨率（2.0-2.5埃）的数据，分布是不切实际的宽。我们的阳离子B-因子与平均B-因子的原子在阳离子环境中的分析表明，大量的结构包含一个不正确的金属离子分配或不寻常的配位模式。还发现了数据分辨率和金属配位球的完整性之间的相关性。（C）2008 Elsevier Inc. All rights reserved.
Analysis of metal-protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal-binding sites in protein structures determined by X-ray crystallography and deposited in the PDB shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion-binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium-resolution structures from the PDB with those from very high-resolution small-molecule structures in the Cambridge Structural Database (CSD). For high-resolution protein structures, the distribution of metal-protein or metal-water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0-2.5 angstrom) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found. (C) 2008 Elsevier Inc. All rights reserved.