Investigation of manganese metal coordination in proteins: a comprehensive PDB analysis and quantum mechanical study

Investigation of manganese metal coordination in proteins: a comprehensive PDB analysis and quantum mechanical study

Manganese (Mn) is an important metal that is crucial in biological cell mechanism and function. However, its binding mechanism is poorly characterized. In the present study, we have carried out a detailed statistical analysis of the Mn-containing proteins through analysis of the metal coordination s...

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Bibliographic Details
Published in:Structural chemistry Vol. 31; no. 3; pp. 1057 - 1064
Main Authors: S., Udayalaxmi, Gangula, Mohan Rao, K., Ravikiran, P., Ettaiah
Format: Journal Article
Language:English
Published: New York Springer US 01-06-2020
Springer Nature B.V
Subjects:
Aspartic acid
Chemistry
Chemistry and Materials Science
Computer Applications in Chemistry
Coordination compounds
Coordination numbers
Crystal structure
Glutamic acid
Manganese
Original Research
Physical Chemistry
Proteins
Quantum mechanics
Statistical analysis
Theoretical and Computational Chemistry
Water chemistry
Coordination sphere
DFT
Quantum mechanical study
Manganese
PDB
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Summary:Manganese (Mn) is an important metal that is crucial in biological cell mechanism and function. However, its binding mechanism is poorly characterized. In the present study, we have carried out a detailed statistical analysis of the Mn-containing proteins through analysis of the metal coordination spheres of the vast number of protein crystal structures present in Protein Data Bank. These results reveal that Mn metal predominantly acquires the coordination number of six and five. In these predominant six and five coordination spheres, Mn metal is majorly stabilized with octahedral and square pyramidal geometries respectively. The water molecules, aspartic acid, and glutamic acid residues bonded frequently with Mn metal ions. These results provided useful insights to characterize the very important Mn-containing subset of the proteome. Quantum mechanical results showed that the complexes with coordination number six are predominantly having high interaction energy, which is in good agreement with statistical analysis.
ISSN:1040-0400
1572-9001
DOI:10.1007/s11224-020-01488-x