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Coordination Number and Geometry

Coordination Number and Geometry

For transition metal complexes, the coordination number determines the geometry around the central metal ion. Table 1 compares coordination numbers to molecular geometry. The most common structures of the complexes in coordination compounds are octahedral, tetrahedral, and square planar.

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...

Molecular Chaperones and Protein Folding

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Molecular Chaperones and Protein Folding

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Allosteric Proteins-ATCase

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...

Colors and Magnetism

Colors and Magnetism

Color in Coordination Complexes
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human eye.

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

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Predicting the coordination number within copper chaperones: Atox1 as case study.

Tamar Ansbacher¹, Avital Shurki

¹Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.

The Journal of Physical Chemistry. B

|April 7, 2012

Summary

Metallochaperone proteins regulate copper ion (Cu(I)) transport using a unique motif. This study developed a computational method to predict copper coordination in these proteins, successfully applied to Atox1.

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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:

Biochemistry
Computational Biology
Biophysics

Background:

Copper ion (Cu(I)) concentration is critical in biological systems and tightly regulated by metallochaperone proteins.
Metallochaperones facilitate intracellular Cu(I) delivery via a conserved (M)XCXXC motif, enabling specific yet efficient metal transfer.

Purpose of the Study:

To establish a computational method for predicting copper coordination numbers in copper chaperones.
To understand the coordination chemistry of Cu(I) within metallochaperones for improved insights into copper transport.

Main Methods:

Development of a novel computational approach to predict copper coordination.
Application and validation of the computational method using the human copper chaperone Atox1.

Main Results:

The developed computational method accurately predicts Cu(I) coordination within Atox1.
The study identified a low coordination number (2-3) for Cu(I) in Atox1, suggesting potential binding of an external ligand.

Conclusions:

A validated computational method for predicting copper coordination in chaperones has been established.
A potential explanation for the unique Cu(I) dicoordination observed in Atox1 is proposed, advancing the understanding of copper homeostasis.