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.

中文翻译：

---

金属蛋白中金属配位距离的数据库概述。


金属蛋白在所有生物体中普遍存在，并参与非常广泛的生物过程。因此，它们的实验表征对于提高对其结构和生物学功能的了解至关重要。三维结构代表了高度相关的信息，因为它提供了对金属离子和蛋白质折叠之间相互作用的洞察。这种相互作用决定了结合金属的化学反应性。由于分辨率差和辐射损伤等实验因素，可用的 PDB 结构可能包含错误。在细化和验证过程中缺乏距离限制也会影响结构质量。在此，我们的目标是通过对基于蛋白质中超过 115,000 个金属结合位点的数据集进行统计分析，全面了解金属离子与其供体原子之间的距离分布。该分析不仅产生了实验人员可以用来支持结构测定过程的参考数据，例如作为细化限制，而且还提高了对不同金属如何发生蛋白质配位及其结合相互作用的性质的深入了解。特别是，检查了羧酸配位的特征，这是几乎所有金属普遍存在的唯一相互作用类型。