Metalloproteins (MPs) play a critical role in numerous biological processes, including catalysis, electron transfer, and structural stabilization, making their structural characterization vital for understanding their function. However, inaccuracies in Protein Data Bank (PDB) entries—caused by poor resolution, radiation damage, and insufficient use of geometric
restraints during refinement—can lead to mischaracterization of metal-binding sites [1,2]. To address this issue, we analyzed 485,000 metal–donor atom distances (non-H atoms within 3 Å directly interacting with the metal) across 115,710 sites using MetalPDB [3,4]. The extensive dataset allowed us to separate metal-binding sites based on resolution ranges. We retained only the data from the 0–1.5 Å resolution range as reference values, since the corresponding metal coordination distances exhibit well-defined peaks compared to the broader distributions observed at lower resolutions. While we did not categorize metal-binding sites according to amino acid composition, our findings revealed distinct preferences for donor atoms and
coordination patterns among metal types. Alkali and alkaline earth metals tend to interact primarily with main-chain oxygen atoms, leading to generally broader metal–donor atoms distances. In contrast, transition metals preferentially coordinate with side-chain atoms, producing sharper and more centered distance distributions. Despite these differences, a common feature across all metal types is their consistent interaction with the carboxylate groups of aspartate and glutamate, underscoring the fundamental role of these residues in metal coordination. To provide a comprehensive analysis, we also examined the distances
between metals and their coordinating water molecules, as well as the distances between metals within polynuclear sites. Our study was further validated through comparisons with MESPEUS and existing literature data [5].
These findings provide reference values at can aid in the determination, refinement, and validation of novel metalloprotein structures, particularly in relation to the diverse configurations that carboxylate groups can adopt during structural determination.
Bibliography
[1] Zheng, H., Chordia, M. D., Cooper, D. R., Chruszcz, M., Müller, P., Sheldrick, G. M. & Minor, W. (2014). Nat. Protoc
[2] Roversi, P. & Tronrud, D. E. (2021). Acta Cryst.
[3] Andreini, C., Cavallaro, G., Lorenzini, S. & Rosato, A. (2013). Nucleic Acids Res.
[4]Andreini, C. & Rosato, A. (2022). Int. J. Mol. Sci. 23, 7684.
[5] Lin, G.-Y., Su, Y.-C., Huang, Y. L. & Hsin, K.-Y. (2024). Nucleic Acids Res