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Updated: Jul 3, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
Data mining of metal ion environments present in protein structures
Heping Zheng1, Maksymilian Chruszcz, Piotr Lasota
1Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.
Structural analysis reveals unusual metal-protein interactions in crystallographic data. This method aids in identifying metal-binding motifs missed by sequence analysis alone, improving protein structure interpretation.
Area of Science:
- Structural Biology
- Biochemistry
- Bioinformatics
Background:
- Metal ions are crucial for protein function, stability, and structure.
- Accurate characterization of metal-protein interactions is vital for understanding biological processes.
- Existing methods may struggle to identify all metal-binding motifs, especially those not evident from sequence alone.
Purpose of the Study:
- To analyze metal-protein interaction parameters (distances, coordination numbers, B-factors, occupancies) in protein data bank (PDB) structures.
- To identify preferences of amino acid residues for specific metal cations.
- To develop a method for rapid identification of metal-binding structural motifs.
Main Methods:
- Analysis of structural data from X-ray crystallography (PDB) and small-molecule crystallography (Cambridge Structural Database - CSD).
- Measurement of amino acid frequencies in metal ion-binding sites.
- Comparison of data from high, medium, and very high-resolution structures.
Main Results:
- Observed unusual values and unexpected correlations in metal-protein interaction parameters.
- Identified residue preferences for specific metal cations.
- Found discrepancies in medium-resolution protein data compared to high-resolution protein and small-molecule data.
- Detected potential issues with metal ion assignment or coordination patterns in numerous structures.
- Established a correlation between data resolution and the completeness of metal coordination spheres.
Conclusions:
- The study highlights potential inaccuracies in deposited protein structures concerning metal ions.
- The developed approach offers a novel way to identify metal-binding sites based on structural features.
- Resolution of crystallographic data significantly impacts the reliability of metal-binding site analysis.
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