Abstract
As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study, we systematically analyzed 3.5 Å regions around all metal ions across all PDB entries with supporting electron density maps available from the PDB in Europe. All resulting metal ion-centric regions were evaluated with respect to four quality-control criteria involving electron density resolution, atom occupancy, symmetry atom exclusion, and regional electron density discrepancy. The resulting list of metal binding sites passing all four criteria possess high regional structural quality and should be beneficial to a wide variety of downstream analyses. This study demonstrates an approach for the pan-PDB evaluation of metal binding site structural quality with respect to underlying X-ray crystallographic experimental data represented in the available electron density maps of proteins. For non-crystallographers in particular, we hope to change the focus and discussion of structural quality from a global evaluation to a regional evaluation, since all structural entries in the wwPDB appear to have both regions of high and low structural quality.
Highlights
Metal ions are important components in biological processes, especially at the biochemical and cellular levels
Our goal is to provide an approach for evaluating metal binding sites against experimental electron density data that could improve the outcomes for a wide variety of downstream structural, dynamic, and functional analyses
As illustrated by previous studies, regional structural quality affects the usability of bound structure, including bound metal ions, for accurately interpreting structural, dynamic, and chemical ligand structure, including bound metal ions, for accurately interpreting structural, dynamic, and properties of ligand binding sites [14,30,31]
Summary
Metal ions are important components in biological processes, especially at the biochemical and cellular levels. An estimated 30% to 40% of proteins across the combined proteome of the biosphere binds at least one metal ion [1,2]. Protein metal binding is part of many biochemical mechanisms including signal transduction, enzyme catalysis, and protein structural integrity [3,4,5]. The quality of 3D protein structural data around metal binding sites can vary dramatically from structure to structure, and especially from region to region [8,11]. When analyzing metal binding site structure and dynamics, the quality of the utilized worldwide
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