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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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Updated: Jun 6, 2025

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

Improving macromolecular structure refinement with metal-coordination restraints.

Kaveh H Babai¹, Fei Long², Martin Malý³

¹Institute of Molecular Biology and Biotechnology, Ministry of Science and Education, 11 Izzat Nabiyev, Baku, Azerbaijan.

Acta Crystallographica. Section D, Structural Biology

|December 3, 2024

Summary

This summary is machine-generated.

Accurately modeling metal coordination in proteins is challenging. This study introduces MetalCoord, a program that analyzes metal-binding geometries from databases, improving structural biology computations.

Keywords:

cryo-EM macromolecular crystallography metal-coordination geometry refinement restraints

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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Published on: September 17, 2017

Area of Science:

Structural biology
Biochemistry
Computational chemistry

Background:

Metals are crucial for protein structure and function.
Accurate modeling of metal coordination geometries is complex and challenging.
Existing methods struggle with the diversity of metal-coordination environments.

Purpose of the Study:

To develop a method for extracting and analyzing metal coordination information.
To create a program (MetalCoord) for classifying and utilizing metal-coordination geometry.
To improve the accuracy of macromolecular structure refinement.

Main Methods:

Extracting coordination data (bond lengths, angles) from the Crystallography Open Database.
Generating stereochemical information using PDB/mmCIF files.
Matching derived metal structures with idealized geometries from a library.
Developing strategies for compiling distance and angle statistics for refinement.

Main Results:

A new program, MetalCoord, was developed and implemented.
MetalCoord effectively classifies and utilizes metal-coordination geometry.
Updated metal-containing components for the CCP4 monomer library were generated.
Derived restraints enhance structural biology computations.

Conclusions:

The MetalCoord program provides a robust method for analyzing metal coordination.
Updated monomer dictionaries and restraints improve macromolecular structure refinement.
The developed methods are applicable to various structural biology techniques like crystallography and cryo-EM.