ArticleJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2008
Statistical analysis of structural characteristics of protein Ca2+-binding sites.
Article in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Review
- MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.Nature communications · 2025Article
- CaProtein science : a publication of the Protein Society · 2025Article
- High-throughput identification of calcium-regulated proteins across diverse proteomes.Cell reports · 2024Article
- Article
- High-Throughput Identification of Calcium Regulated Proteins Across Diverse Proteomes.bioRxiv : the preprint server for biology · 2024Article
- Drastic alterations in the loop structure around colchicine upon complex formation with an engineered lipocalin indicate a conformational selection mechanism.Acta crystallographica. Section F, Structural biology communications · 2023Article
- Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase.Frontiers in molecular biosciences · 2022Article
- Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins.The journal of physical chemistry. B · 2021Article
- Structural Aspects and Prediction of Calmodulin-Binding Proteins.International journal of molecular sciences · 2020Review
- International Union of Basic and Clinical Pharmacology. CVIII. Calcium-Sensing Receptor Nomenclature, Pharmacology, and Function.Pharmacological reviews · 2020Review
- Design of Calcium-Binding Proteins to Sense Calcium.Molecules (Basel, Switzerland) · 2020Review
- Designing Calcium-Binding Proteins for Molecular MR Imaging.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Calcium-Binding Proteins with Disordered Structure and Their Role in Secretion, Storage, and Cellular Signaling.Biomolecules · 2018Review
- Calcium Dynamics Mediated by the Endoplasmic/Sarcoplasmic Reticulum and Related Diseases.International journal of molecular sciences · 2017Review
- Molecular Basis for Modulation of Metabotropic Glutamate Receptors and Their Drug Actions by Extracellular CaInternational journal of molecular sciences · 2017Review
- Defining potential roles of Pb(2+) in neurotoxicity from a calciomics approach.Metallomics : integrated biometal science · 2016Review
- UCP3 is associated with Hax-1 in mitochondria in the presence of calcium ion.Biochemical and biophysical research communications · 2016Article
- Molecular Basis of S100A1 Activation at Saturating and Subsaturating Calcium Concentrations.Biophysical journal · 2016Article
- An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels.Nature communications · 2016Article
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Authors and funding
6 authors.
Funding
Abstract
To better understand the biological significance of Ca(2+), we report a comprehensive statistical analysis of calcium-binding proteins from the Protein Data Bank to identify structural parameters associated with EF-hand and non-EF-hand Ca(2+)-binding sites. Comparatively, non-EF-hand sites utilize lower coordination numbers (6 +/- 2 vs. 7 +/- 1), fewer protein ligands (4 +/- 2 vs. 6 +/- 1), and more water ligands (2 +/- 2 vs. 1 +/- 0) than EF-hand sites. The orders of ligand preference for non-EF-hand and EF-hand sites, respectively, were H(2)O (33.1%) > side-chain Asp (24.5%) > main-chain carbonyl (23.9%) > side-chain Glu (10.4%), and side-chain Asp (29.7%) > side-chain Glu (26.6%) > main-chain carbonyl (21.4%) > H(2)O (13.3%). Less formal negative charge was observed in the non-EF-hand than in the EF-hand binding sites (1 +/- 1 vs. 3 +/- 1). Additionally, over 20% of non-EF-hand sites had formal charge values of zero due to increased utilization of water and carbonyl oxygen ligands. Moreover, the EF-hand sites presented a narrower range of ligand distances and bond angles than non-EF-hand sites, possibly owing to the highly conserved helix-loop-helix motif. Significant differences between ligand types (carbonyl, side chain, bidentate) demonstrated that angles associated with each type must be classified separately, and the EF-hand side-chain Ca-O-C angles exhibited an unusual bimodal quality consistent with an Asp distribution that differed from the Gaussian model observed for non-EF-hand proteins. The results of this survey more accurately describe differences between EF-hand and non-EF-hand proteins and provide new parameters for the prediction and design of different classes of Ca(2+)-binding proteins.
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