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Metal-Ligand Bonds

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

CheckMyMetal: a macromolecular metal-binding validation tool.

Heping Zheng¹, David R Cooper¹, Przemyslaw J Porebski¹

¹Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Acta Crystallographica. Section D, Structural Biology

|March 15, 2017

Summary

This summary is machine-generated.

CheckMyMetal (CMM) is a free web server that validates metal-binding sites in macromolecular structures. It identifies errors in metal assignments and geometry, improving structural biology data quality.

Keywords:

CheckMyMetal coordination geometry metal-binding environment validation

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

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Area of Science:

Structural Biology
Biochemistry
Computational Biology

Background:

Metal ions are crucial for numerous biological functions, present in approximately 40% of Protein Data Bank (PDB) macromolecular structures.
A notable proportion of these structures exhibit inadequately modeled metal-binding sites, impacting data reliability.

Purpose of the Study:

To introduce CheckMyMetal (CMM), a user-friendly web server for validating metal-binding sites in macromolecules.
To provide guidelines and practical examples for metal-site modeling and validation.

Main Methods:

Development of the CheckMyMetal (CMM) web server, accessible at http://csgid.org/csgid/metal_sites.
Implementation of algorithms to detect incorrect metal assignments and geometrical irregularities in metal-binding sites.
Compilation of illustrative examples categorized by metal type to guide users.

Main Results:

CMM effectively identifies errors in metal assignments and geometric issues within metal-binding sites.
The server provides a practical tool for researchers to assess and improve the quality of metal-site modeling.
Demonstrated common pitfalls in metal-site modeling through diverse examples.

Conclusions:

CheckMyMetal (CMM) serves as a valuable resource for validating metal-binding sites in macromolecular structures.
The tool aids crystallographers and structural biologists in refining metal-site modeling accuracy.
Promotes higher quality structural data in the Protein Data Bank (PDB).