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

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Abstract

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.

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Acknowledgments

Authors wish to thank Management and Department of Chemistry, CKM Arts and Science College, Warangal, Qstatix Pvt. Ltd., Hyderabad and Osmania University, Hyderabad, for providing facilities.

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Correspondence to Mohan Rao Gangula.

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S., U., Gangula, M.R., K., R. et al. Investigation of manganese metal coordination in proteins: a comprehensive PDB analysis and quantum mechanical study. Struct Chem (2020). https://doi.org/10.1007/s11224-020-01488-x

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Keywords

  • Manganese
  • PDB
  • Quantum mechanical study
  • Coordination sphere
  • DFT