ArticleActa crystallographica. Section D, Structural biology2016
Validation and correction of Zn-Cys
Article in Acta crystallographica. Section D, Structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Conformational dynamics in specialized CProtein science : a publication of the Protein Society · 2025Article
- Improving macromolecular structure refinement with metal-coordination restraints.Acta crystallographica. Section D, Structural biology · 2024Article
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- 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
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- The missing link: covalent linkages in structural models.Acta crystallographica. Section D, Structural biology · 2021Article
- Modelling covalent linkages in CCP4.Acta crystallographica. Section D, Structural biology · 2021Article
- Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2.Viruses · 2021Article
- LAHMA: structure analysis through local annotation of homology-matched amino acids.Acta crystallographica. Section D, Structural biology · 2021Article
- Local and global analysis of macromolecular atomic displacement parameters.Acta crystallographica. Section D, Structural biology · 2020Article
- Non-native fold of the putative VPS39 zinc finger domain.Wellcome open research · 2020Article
- Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.Nature structural & molecular biology · 2018Article
- ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.Acta crystallographica. Section D, Structural biology · 2018Article
- Homology-based hydrogen bond information improves crystallographic structures in the PDB.Protein science : a publication of the Protein Society · 2018Article
- An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein.The Journal of biological chemistry · 2018Article
- CheckMyMetal: a macromolecular metal-binding validation tool.Acta crystallographica. Section D, Structural biology · 2017Article
- AceDRG: a stereochemical description generator for ligands.Acta crystallographica. Section D, Structural biology · 2017Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn-Cys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.
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