Manganese in the structure of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans (pdb 2cdy)

The binding sites of Manganese atom in the structure of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans (pdb code 2cdy). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2cdy structure was solved by R.DENNIS, E.MICOSSI, J.MCCARTHY, E.MOE, E.GORDON, G.LEONARD, S.MCSWEENEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.2-2.0 Space group P1211 a (A) 43.577 b (A) 87.100 c (A) 116.418 alpha (°) 90.00 beta (°) 92.10 gamma (°) 90.00 Rfactor (%) 17.3 Rfree (%) 22.1 Manganese Binding Sites: Manganese binding site 1 out of 4 in 2cdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2cdy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His26, A: His80, A: Trp133, A: Gln151, A: Asp172, A: Trp174, A: His176, A: Ala177, A: Hoh2183, conact list: Atom Atom Distance (A) Mn NE2 A:His26 2.24 Mn ND1 A:His26 4.34 Mn CD2 A:His26 3.18 Mn CE1 A:His26 3.23 Mn CG A:His26 4.35 Mn NE2 A:His80 2.15 Mn ND1 A:His80 4.22 Mn CD2 A:His80 3.18 Mn CE1 A:His80 3.07 Mn CG A:His80 4.30 Mn CZ2 A:Trp133 4.40 Mn CH2 A:Trp133 4.97 Mn NE2 A:Gln151 4.59 Mn CB A:Asp172 4.26 Mn OD2 A:Asp172 1.92 Mn OD1 A:Asp172 3.53 Mn CG A:Asp172 3.03 Mn CB A:Trp174 4.58 Mn CG A:Trp174 4.77 Mn NE2 A:His176 2.24 Mn ND1 A:His176 4.34 Mn CD2 A:His176 3.19 Mn CE1 A:His176 3.23 Mn CG A:His176 4.35 Mn CB A:Ala177 4.90 Mn O A:Hoh2183 2.26 interactive model: Manganese binding site 2 out of 4 in 2cdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2cdy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His26, B: His80, B: Trp133, B: Gln151, B: Asp172, B: Trp174, B: His176, B: Ala177, B: Hoh2100, conact list: Atom Atom Distance (A) Mn NE2 B:His26 2.17 Mn ND1 B:His26 4.22 Mn CD2 B:His26 3.19 Mn CE1 B:His26 3.08 Mn CG B:His26 4.30 Mn NE2 B:His80 2.11 Mn ND1 B:His80 4.19 Mn CD2 B:His80 3.10 Mn CE1 B:His80 3.07 Mn CG B:His80 4.23 Mn CZ2 B:Trp133 4.45 Mn NE2 B:Gln151 4.47 Mn CB B:Asp172 4.25 Mn OD2 B:Asp172 1.93 Mn OD1 B:Asp172 3.51 Mn CG B:Asp172 3.03 Mn CB B:Trp174 4.63 Mn CG B:Trp174 4.77 Mn NE2 B:His176 2.31 Mn ND1 B:His176 4.42 Mn CD2 B:His176 3.23 Mn CE1 B:His176 3.32 Mn CG B:His176 4.41 Mn CB B:Ala177 4.96 Mn O B:Hoh2100 2.21 interactive model: Manganese binding site 3 out of 4 in 2cdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2cdy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His26, C: His80, C: Trp133, C: Gln151, C: Asp172, C: Trp174, C: His176, C: Ala177, C: Hoh2120, conact list: Atom Atom Distance (A) Mn NE2 C:His26 2.21 Mn ND1 C:His26 4.28 Mn CD2 C:His26 3.19 Mn CE1 C:His26 3.17 Mn CG C:His26 4.32 Mn NE2 C:His80 2.13 Mn ND1 C:His80 4.21 Mn CD2 C:His80 3.14 Mn CE1 C:His80 3.08 Mn CG C:His80 4.27 Mn CZ2 C:Trp133 4.39 Mn CH2 C:Trp133 4.98 Mn NE2 C:Gln151 4.55 Mn CB C:Asp172 4.30 Mn OD2 C:Asp172 1.93 Mn OD1 C:Asp172 3.43 Mn CG C:Asp172 3.01 Mn CB C:Trp174 4.56 Mn CD1 C:Trp174 4.94 Mn CG C:Trp174 4.71 Mn NE2 C:His176 2.20 Mn ND1 C:His176 4.30 Mn CD2 C:His176 3.16 Mn CE1 C:His176 3.19 Mn CG C:His176 4.32 Mn CB C:Ala177 4.91 Mn O C:Hoh2120 2.20 interactive model: Manganese binding site 4 out of 4 in 2cdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2cdy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His26, D: His80, D: Trp133, D: Gln151, D: Asp172, D: Trp174, D: His176, D: Ala177, D: Hoh2164, conact list: Atom Atom Distance (A) Mn NE2 D:His26 2.21 Mn ND1 D:His26 4.30 Mn CD2 D:His26 3.16 Mn CE1 D:His26 3.19 Mn CG D:His26 4.31 Mn NE2 D:His80 2.12 Mn ND1 D:His80 4.20 Mn CD2 D:His80 3.12 Mn CE1 D:His80 3.08 Mn CG D:His80 4.25 Mn CZ2 D:Trp133 4.39 Mn CH2 D:Trp133 4.98 Mn NE2 D:Gln151 4.58 Mn CB D:Asp172 4.29 Mn OD2 D:Asp172 1.98 Mn OD1 D:Asp172 3.49 Mn CG D:Asp172 3.04 Mn CB D:Trp174 4.65 Mn CG D:Trp174 4.78 Mn NE2 D:His176 2.31 Mn ND1 D:His176 4.41 Mn CD2 D:His176 3.25 Mn CE1 D:His176 3.31 Mn CG D:His176 4.42 Mn CB D:Ala177 4.90 Mn O D:Hoh2164 2.25 interactive model: