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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
Geometry of metal-ligand interactions in proteins
1Institute of Cell and Molecular Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3JR, Scotland. marjorie.harding@ed.ac.uk
Acta Crystallographica. Section D, Biological Crystallography
|February 27, 2001
Summary
This study compares metal-ligand geometry in proteins and small molecules. Cambridge Structural Database (CSD) data offers valuable targets for refining metalloprotein structures, especially for metal-donor distances.
Area of Science:
- Structural Biology
- Bioinorganic Chemistry
- Crystallography
Background:
- Understanding metal-ligand interactions is crucial in metalloproteins.
- The Cambridge Structural Database (CSD) provides extensive data on small-molecule complexes.
- Protein Data Bank (PDB) archives diverse metalloprotein structures.
Purpose of the Study:
- To compare metal-ligand geometry in proteins with small-molecule complexes.
- To assess the predictive power of CSD data for metalloprotein structures.
- To establish guidelines for using CSD-derived restraints in protein structure refinement.
Main Methods:
- Analysis of metal-donor atom distances, coordination numbers, and geometry distortions.
- Comparison of PDB metalloprotein structures (resolution ≤ 1.6 Å) with CSD data.
- Evaluation of CSD-derived restraints for metal-donor distances and angles.
Main Results:
- Good agreement between PDB and CSD geometries for high-resolution protein structures.
- Poorer agreement for lower-resolution protein structures (up to 2.8 Å).
- CSD-derived metal-donor distances serve as effective targets for validation and refinement.
- Zn-carboxylate coordination shows a continuous range from monodentate to bidentate, observed in both CSD and PDB data.
Conclusions:
- CSD data provides valuable, adjustable targets for metal-donor distances in metalloprotein refinement.
- Angle restraints are more challenging due to inherent flexibility but simplified parameters are provided.
- Specific coordination patterns, like Zn-carboxylate interactions, are conserved across small molecules and proteins.
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