蛋白质数据库
金属蛋白
蛋白质数据库
生物系统
计算机科学
金属
化学
过程(计算)
羧酸盐
蛋白质结构
计算化学
生物
立体化学
生物化学
操作系统
有机化学
作者
Milana Bazayeva,Claudia Andreini,Antonio Rosato
出处
期刊:
日期:2024-04-29
卷期号:80 (5): 362-376
被引量:7
标识
DOI:10.1107/s2059798324003152
摘要
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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