Details

Autor(en) / Beteiligte

• Bazayeva, Milana
• Andreini, Claudia
• Rosato, Antonio

Titel

A database overview of metal‐coordination distances in metalloproteins

Ist Teil von

• Acta crystallographica. Section D, Biological crystallography., 2024-05, Vol.80 (5), p.362-376

Ort / Verlag

5 Abbey Square, Chester, Cheshire CH1 2HU, England: International Union of Crystallography

Erscheinungsjahr

2024

Quelle

Wiley-Blackwell Journals

Beschreibungen/Notizen

• 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. Through the analysis of more than 115 000 metal‐binding sites in metalloproteins, experimentalists are offered useful reference data that improve the understanding of metal‐binding interactions and protein coordination. Carboxylate coordination, which is common for a variety of metals, is especially highlighted.