ReviewInternational journal of molecular sciences2016
Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics.
Review in International journal of molecular sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed.
- Review
- Cysteine-rich zinc finger proteins and the nuclear factor kappa-B pathway.Frontiers in chemical biology · 2024Article
- The zinc proteome of SARS-CoV-2.Metallomics : integrated biometal science · 2022Article
- Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications.International journal of molecular sciences · 2022Review
- A New Paradigm of Multiheme Cytochrome Evolution by Grafting and Pruning Protein Modules.Molecular biology and evolution · 2022Article
- Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer.Science advances · 2022Article
- XANES Measurements for Studies of Adsorbed Protein Layers at Liquid Interfaces.Materials (Basel, Switzerland) · 2020Article
- Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii.Cell chemical biology · 2019Article
- The cellular economy of the Saccharomyces cerevisiae zinc proteome.Metallomics : integrated biometal science · 2018Article
- To what extent do structural changes in catalytic metal sites affect enzyme function?Journal of inorganic biochemistry · 2018Article
- MetalPDB in 2018: a database of metal sites in biological macromolecular structures.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity.
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