Manganese in the structure of Crystal Structure of the Metal-Bound Superoxide Dismutase From Pyrobaculum Aerophilum (pdb 3evk)

The binding sites of Manganese atom in the structure of Crystal Structure of the Metal-Bound Superoxide Dismutase From Pyrobaculum Aerophilum (pdb code 3evk). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3evk structure was solved by S.LEE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.5-1.9 Space group P3221 a (A) 94.909 b (A) 94.909 c (A) 171.890 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.2 Rfree (%) 23 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3evk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3evk. 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: His42, A: Tyr50, A: His90, A: Trp141, A: His161, A: Asp176, A: Trp178, A: His180, A: Ala181, A: Hoh302, conact list: Atom Atom Distance (A) Mn NE2 A:His42 2.26 Mn ND1 A:His42 4.32 Mn CD2 A:His42 3.14 Mn CE1 A:His42 3.26 Mn CG A:His42 4.30 Mn CE2 A:Tyr50 4.82 Mn OH A:Tyr50 4.88 Mn NE2 A:His90 2.32 Mn ND1 A:His90 4.29 Mn CD2 A:His90 3.45 Mn CE1 A:His90 3.08 Mn CG A:His90 4.49 Mn CZ2 A:Trp141 4.56 Mn CH2 A:Trp141 4.84 Mn NE2 A:His161 4.80 Mn CB A:Asp176 4.36 Mn OD2 A:Asp176 2.02 Mn OD1 A:Asp176 3.53 Mn CG A:Asp176 3.10 Mn CB A:Trp178 4.33 Mn CD1 A:Trp178 4.78 Mn CG A:Trp178 4.52 Mn NE2 A:His180 2.39 Mn ND1 A:His180 4.51 Mn CD2 A:His180 3.20 Mn CE1 A:His180 3.46 Mn CG A:His180 4.42 Mn CB A:Ala181 4.88 Mn O A:Hoh302 1.95 interactive model: Manganese binding site 2 out of 4 in 3evk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3evk. 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: His42, B: His90, B: Trp141, B: Asp176, B: Trp178, B: His180, B: Ala181, B: Hoh302, conact list: Atom Atom Distance (A) Mn NE2 B:His42 2.11 Mn ND1 B:His42 4.17 Mn CD2 B:His42 3.08 Mn CE1 B:His42 3.07 Mn CG B:His42 4.21 Mn NE2 B:His90 2.47 Mn ND1 B:His90 4.44 Mn CD2 B:His90 3.56 Mn CE1 B:His90 3.25 Mn CG B:His90 4.62 Mn CZ2 B:Trp141 4.61 Mn CH2 B:Trp141 4.86 Mn CB B:Asp176 4.08 Mn OD2 B:Asp176 1.75 Mn OD1 B:Asp176 3.42 Mn CG B:Asp176 2.88 Mn CB B:Trp178 4.27 Mn CD1 B:Trp178 4.82 Mn CG B:Trp178 4.53 Mn NE2 B:His180 2.48 Mn ND1 B:His180 4.55 Mn CD2 B:His180 3.32 Mn CE1 B:His180 3.49 Mn CG B:His180 4.50 Mn CB B:Ala181 4.61 Mn O B:Hoh302 2.24 interactive model: Manganese binding site 3 out of 4 in 3evk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3evk. 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: His42, C: His46, C: Tyr50, C: His90, C: Trp141, C: His161, C: Asp176, C: Trp178, C: His180, C: Ala181, C: Hoh302, conact list: Atom Atom Distance (A) Mn NE2 C:His42 2.12 Mn ND1 C:His42 4.18 Mn CD2 C:His42 3.04 Mn CE1 C:His42 3.11 Mn CG C:His42 4.17 Mn CB C:His46 4.98 Mn CE2 C:Tyr50 4.84 Mn OH C:Tyr50 4.84 Mn NE2 C:His90 2.38 Mn ND1 C:His90 4.28 Mn CD2 C:His90 3.57 Mn CE1 C:His90 3.03 Mn CG C:His90 4.56 Mn CZ2 C:Trp141 4.63 Mn CH2 C:Trp141 4.90 Mn NE2 C:His161 4.88 Mn CB C:Asp176 4.41 Mn OD2 C:Asp176 2.06 Mn OD1 C:Asp176 3.54 Mn CG C:Asp176 3.14 Mn CB C:Trp178 4.34 Mn CD1 C:Trp178 4.85 Mn CG C:Trp178 4.57 Mn NE2 C:His180 2.40 Mn ND1 C:His180 4.51 Mn CD2 C:His180 3.16 Mn CE1 C:His180 3.50 Mn CG C:His180 4.38 Mn CB C:Ala181 4.80 Mn O C:Hoh302 1.90 interactive model: Manganese binding site 4 out of 4 in 3evk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3evk. 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: His42, D: His46, D: Tyr50, D: His90, D: Trp141, D: His161, D: Asp176, D: Trp178, D: His180, conact list: Atom Atom Distance (A) Mn NE2 D:His42 2.31 Mn ND1 D:His42 4.44 Mn CD2 D:His42 2.96 Mn CE1 D:His42 3.48 Mn CG D:His42 4.23 Mn CB D:His46 4.68 Mn CE2 D:Tyr50 4.41 Mn CZ D:Tyr50 4.96 Mn OH D:Tyr50 4.46 Mn NE2 D:His90 2.09 Mn ND1 D:His90 4.05 Mn CD2 D:His90 3.26 Mn CE1 D:His90 2.85 Mn CG D:His90 4.28 Mn CZ2 D:Trp141 4.74 Mn NE2 D:His161 4.75 Mn CB D:Asp176 4.78 Mn OD2 D:Asp176 2.50 Mn OD1 D:Asp176 4.10 Mn CG D:Asp176 3.60 Mn CB D:Trp178 4.83 Mn CG D:Trp178 4.92 Mn NE2 D:His180 2.32 Mn ND1 D:His180 4.42 Mn CD2 D:His180 3.29 Mn CE1 D:His180 3.30 Mn CG D:His180 4.45 interactive model: