ArticleJournal of molecular modeling2011
Metals in proteins: cluster analysis studies.
Article in Journal of molecular modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 11 citations in OpenAlex.
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network.Journal of chemical information and modeling · 2022Review
- Benchmark of Density Functionals for the Calculation of the Redox Potential of FeFrontiers in chemistry · 2019Article
- Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns.Journal of molecular modeling · 2014Article
- An approach to crystallizing proteins by metal-mediated synthetic symmetrization.Protein science : a publication of the Protein Society · 2011Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have conducted a prospective analysis of the Protein Data Bank in order to study certain constituents of proteins: elements that are neither halogens nor phosphorus nor part of the biological amino acid set. A sample of 5749 structures was analyzed and classified according to the 56 elements encountered. Fifteen metals (Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, W, Hg) are involved in almost half of the structures, with each metal figuring in more than 100 structures. We analyzed this subsample in more detail by computing the amino acid residues occurring within a coordination sphere of 5 Å centered on the element, and using methods of cluster analysis to group the elements. The analyses undertaken here are able to distinguish between real components of proteins and elements inserted by artefacts of the crystallization process or experimental techniques.
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Registered trials
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