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Related Concept Videos

Coordination Number and Geometry02:57

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 Bonds02:51

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...
Valence Bond Theory02:42

Valence Bond Theory

Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
Ionic Crystal Structures02:42

Ionic Crystal Structures

Ionic crystals consist of two or more different kinds of ions that usually have different sizes. The packing of these ions into a crystal structure is more complex than the packing of metal atoms that are the same size.
Most monatomic ions behave as charged spheres, and their attraction for ions of opposite charge is the same in every direction. Consequently, stable structures for ionic compounds result (1) when ions of one charge are surrounded by as many ions as possible of the opposite...
Coordination Compounds and Nomenclature02:54

Coordination Compounds and Nomenclature

In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...

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Preparation of SNS Cobalt(II) Pincer Model Complexes of Liver Alcohol Dehydrogenase
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Preparation of SNS Cobalt(II) Pincer Model Complexes of Liver Alcohol Dehydrogenase

Published on: March 19, 2020

Zinc coordination spheres in protein structures.

Mikko Laitaoja1, Jarkko Valjakka, Janne Jänis

  • 1University of Eastern Finland , Department of Chemistry, P.O. Box 111, FI-80101 Joensuu, Finland.

Inorganic Chemistry
|September 25, 2013
PubMed
Summary

This study reveals that many zinc ions in protein crystal structures are artifacts, not biologically relevant. A stable zinc coordination sphere requires at least four ligands in a tetrahedral geometry.

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Published on: September 7, 2019

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinorganic Chemistry

Background:

  • Zinc metalloproteins are abundant and diverse, playing crucial roles in protein folding, catalysis, and oligomerization.
  • Previous database surveys on zinc proteins have limitations and misinterpretations.
  • Understanding zinc coordination chemistry in proteins is vital for biological insights.

Purpose of the Study:

  • To provide a comprehensive and up-to-date analysis of zinc coordination environments in proteins.
  • To identify potential misinterpretations in existing protein data bank (PDB) structural data.
  • To clarify the biological significance and structural characteristics of zinc ions in proteins.

Main Methods:

  • Detailed analysis of zinc-containing protein structures from the Protein Data Bank (PDB).
  • Statistical analysis of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification.
  • Evaluation of potential sources of error in structural data, such as symmetry-related molecules and missing electron densities.

Main Results:

  • Identified a wide range of zinc coordination spheres, from simple tetrahedral sites to complex binuclear sites.
  • Found that hundreds of PDB structures may have misinterpreted zinc coordination environments.
  • Observed an increase in average metal-to-ligand bond length with higher crystallographic resolution.
  • Determined that approximately one-third of observed zinc ions are crystallographic artifacts with no biological function.

Conclusions:

  • A minimal stable zinc coordination sphere consists of four ligands with tetrahedral geometry.
  • Crystallographic resolution and potential artifacts must be considered when analyzing zinc binding sites.
  • This study offers a more accurate understanding of zinc's role in protein structure and function.