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

  • Udayalaxmi S.
  • Mohan Rao GangulaEmail author
  • Ravikiran K.
  • Ettaiah P.
Original Research


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.


Manganese PDB Quantum mechanical study Coordination sphere DFT 



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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. 1.
    Harding MM, Nowicki MW, Walkinshaw MD (2010) Metals in protein structures: a review of their principal features. Crystallogr Rev 16:247–302CrossRefGoogle Scholar
  2. 2.
    Lu Y (2006) Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges. Inorg Chem 45:9930–9940CrossRefGoogle Scholar
  3. 3.
    Pidcock E, Moore GR (2001) Structural characteristics of protein binding sites for calcium and lanthanide ions. J Biol Inorg Chem 6:479–489CrossRefGoogle Scholar
  4. 4.
    Dismukes GC (1996) Manganese enzymes with binuclear active sites. Chem Rev 96:2909–2926CrossRefGoogle Scholar
  5. 5.
    Lipscomb WN, Strater N (1996) Recent advances in zinc enzymology. Chem Rev 96:2375–2434CrossRefGoogle Scholar
  6. 6.
    Berg JM, Godwin HA (1997) Lessons from zinc-binding peptides. Annu Rev Biophys Biomol Struct 26:357–371CrossRefGoogle Scholar
  7. 7.
    Dokmanić I, Sikić M, Tomić S (2008) Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination. Acta Crystallogr D Biol Crystallogr 64:257–263CrossRefGoogle Scholar
  8. 8.
    Maret W (2010) Metalloproteomics, metalloproteomes, and the annotation of metalloproteins. Metallomics 2:117–125CrossRefGoogle Scholar
  9. 9.
    Christianson DW (1997) Structural chemistry and biology of manganese metalloenzymes. Prog Biophys Mol Biol 67:217–252CrossRefGoogle Scholar
  10. 10.
    Cotton FA, Wilkinson G (1980) Advanced inorganic chemistry. A comprehensive text4th edn. Wiley, New YorkGoogle Scholar
  11. 11.
    Frau’sto da Silva JJR, Williams RJP (1991) The biological chemistry of the elements. The Inorganic Chemistry of Life Clarendon Press, OxfordGoogle Scholar
  12. 12.
    Rulísek L, Vondrásek J (1998) Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins. J Inorg Biochem 71:115–127CrossRefGoogle Scholar
  13. 13.
    Harding MM (2004) The architecture of metal coordination groups in proteins. Acta Crystallogr D Biol Crystallogr 60:849–859CrossRefGoogle Scholar
  14. 14.
    Harding MM (2001) Geometry of metal-ligand interactions in proteins. Acta Crystallogr D Biol Crystallogr 57:401–411CrossRefGoogle Scholar
  15. 15.
    Harding MM (1999) The geometry of metal-ligand interactions relevant to proteins. Acta Crystallogr D Biol Crystallogr 55:1432–1443CrossRefGoogle Scholar
  16. 16.
    Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W (2008) Data mining of metal ion environments present in protein structures. J Inorg Biochem 102:1765–1776CrossRefGoogle Scholar
  17. 17.
    Mahadevi AS, Sastry GN (2013) Cation-π interaction: its role and relevance in chemistry, biology and material science. Chem Rev 113:2100–2138CrossRefGoogle Scholar
  18. 18.
    Hsin K, Sheng Y, Harding MM, Taylor P, Walkinshaw MD (2008) MESPEUS: a database of the geometry of metal sites in proteins. J Appl Crystallogr 41:963–968CrossRefGoogle Scholar
  19. 19.
    Hemavathi K, Kalaivani M, Udayakumar A, Sowmiya G, Jeyakanthan J, Sekar K (2009) MIPS: metal interactions in protein structures. J Appl Crystallogr 43:196–199CrossRefGoogle Scholar
  20. 20.
    Tus A, Rakipovic A, Peretin G, Tomic S, Sikic M (2012) BioMe: biologically relevant metals. Nucleic Acids Res 40:W352–W357CrossRefGoogle Scholar
  21. 21.
    Brylinski M, Skolnick J (2011) FINDSITE-metal: integrating evolutionary information and machine learning for structure based metal-binding site prediction at the proteome level. Proteins 79:735–751CrossRefGoogle Scholar
  22. 22.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian09, Revision A02. Gaussian, Inc, WallingfordGoogle Scholar
  23. 23.
    Ziegler T (1991) Approximate density functional theory as a practical tool in molecular energetics and dynamics. Chem Rev 91:651–667CrossRefGoogle Scholar
  24. 24.
    Andrae D, Haussermann U, Dolg M, Stoll H, Preuss H (1990). Theor Chim Acta 77:123–141CrossRefGoogle Scholar
  25. 25.
    Dunning, TH, Hay PJ (1997) Modern Theoretical Chemistry Plenum New YorkGoogle Scholar
  26. 26.
    Dolg M, Wedig U, Stoll H, Preuss H (1987) Energy-adjusted ab initio pseudo potentials for the first row transition elements. J Chem Phys 86:866CrossRefGoogle Scholar
  27. 27.
    Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113:6378–6396CrossRefGoogle Scholar
  28. 28.
    Purushotham U, Takenaka N, Nagaoka M (2016) Additive effect of fluoroethylene and difluoroethylene carbonates for the solid electrolyte interphase film formation in sodium-ion batteries: a quantum chemical study. RSC Adv 6:65232–65242CrossRefGoogle Scholar
  29. 29.
    Blomberg MRA, Siegbahn PEM, Babcock GT (1998) Modeling electron transfer in biochemistry: A quantum chemical study of charge separation in Rhodobacter sphaeroides and Photosystem II. J Am Chem Soc 120:8812–8824CrossRefGoogle Scholar
  30. 30.
    Siegbahn PEM (1998) Theoretical study of the substrate mechanism of Ribonucleotide Reductase. J Am Chem Soc 120:8417–8429CrossRefGoogle Scholar
  31. 31.
    Purushotham U (2018) Exploration of conformations, Analysis of Protein and Biological Significance of Histidine Dimers. Chemistry Select 3:3070Google Scholar
  32. 32.
    Tanneeru K, Guruprasad L (2013) Structural basis for binding of aurora-AG198N-INCENP complex: MD simulations and free energy calculations. Protein Pept Lett 20:1246–1256CrossRefGoogle Scholar
  33. 33.
    Tanneeru K, Sahu I, Guruprasad L (2013) Ligand-based drug design for human endothelin converting enzyme-1 inhibitors. Med Chem Res 22:4401–4409CrossRefGoogle Scholar
  34. 34.
    Purushotham U, Zipse H, Sastry GN (2016) A first-principles investigation of histidine and its ionic counterparts. Theor Chem Acc 135:174–190CrossRefGoogle Scholar
  35. 35.
    Kaufman Katz A, Shimoni-Livny L, Navon O, Navon N, Bock CW, Glusker JP (2003) Copper-binding motifs: Structural and theoretical aspects. Helv Chim Acta 86:1320–1338CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Research Center, Department of ChemistryC.K.M. Arts and Science College (Kakatiya University)WarangalIndia
  2. 2.Department of ChemistryOsmania UniversityHyderabadIndia

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