Manganese in the structure of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf (pdb 4dr0)

The binding sites of Manganese atom in the structure of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf (pdb code 4dr0). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 4dr0 structure was solved by A.K.BOAL, J.A.COTRUVO JR., J.STUBBE, A.C.ROSENZWEIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.3-1.9 Space group P21212 a (A) 110.525 b (A) 112.912 c (A) 51.286 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 22.4 Manganese Binding Sites: Manganese binding site 1 out of 4 in 4dr0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 4dr0. 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: Asp66, A: Gln69, A: Glu97, A: His101, A: Glu164, A: Phe168, A: Glu198, A: His201, A: Mn402, conact list: Atom Atom Distance (A) Mn OD1 A:Asp66 4.93 Mn NE2 A:Gln69 4.76 Mn CG A:Gln69 4.44 Mn OE1 A:Glu97 3.04 Mn OE2 A:Glu97 1.96 Mn CD A:Glu97 2.84 Mn CG A:Glu97 4.24 Mn CE1 A:His101 4.95 Mn OE1 A:Glu164 2.13 Mn CB A:Glu164 4.76 Mn OE2 A:Glu164 1.97 Mn CD A:Glu164 2.34 Mn CG A:Glu164 3.87 Mn CE2 A:Phe168 4.57 Mn N A:Glu198 4.96 Mn OE1 A:Glu198 2.17 Mn CB A:Glu198 4.40 Mn OE2 A:Glu198 4.10 Mn CD A:Glu198 3.37 Mn CG A:Glu198 4.44 Mn CA A:Glu198 4.24 Mn NE2 A:His201 4.48 Mn CB A:His201 3.54 Mn ND1 A:His201 2.41 Mn CD2 A:His201 4.49 Mn CE1 A:His201 3.38 Mn CG A:His201 3.34 Mn MN A:Mn402 3.74 interactive model: Manganese binding site 2 out of 4 in 4dr0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 4dr0. 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: Asp66, A: Glu97, A: His101, A: Glu164, A: Phe168, A: Ile194, A: Glu198, A: Mn401, conact list: Atom Atom Distance (A) Mn CB A:Asp66 4.29 Mn OD2 A:Asp66 3.12 Mn OD1 A:Asp66 2.03 Mn CG A:Asp66 2.90 Mn CA A:Asp66 4.89 Mn O A:Glu97 4.84 Mn N A:Glu97 4.89 Mn OE1 A:Glu97 2.11 Mn CB A:Glu97 4.48 Mn OE2 A:Glu97 3.73 Mn CD A:Glu97 3.19 Mn CG A:Glu97 4.39 Mn CA A:Glu97 4.16 Mn NE2 A:His101 4.23 Mn CB A:His101 3.61 Mn ND1 A:His101 2.18 Mn CD2 A:His101 4.33 Mn CE1 A:His101 3.07 Mn CG A:His101 3.24 Mn OE1 A:Glu164 4.95 Mn CE2 A:Phe168 4.21 Mn CZ A:Phe168 3.90 Mn CE1 A:Phe168 4.77 Mn CG2 A:Ile194 4.39 Mn OE1 A:Glu198 2.71 Mn OE2 A:Glu198 2.10 Mn CD A:Glu198 2.73 Mn CG A:Glu198 4.20 Mn MN A:Mn401 3.74 interactive model: Manganese binding site 3 out of 4 in 4dr0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 4dr0. 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: Asp66, B: Gln69, B: Met74, B: Glu97, B: His101, B: Glu164, B: Phe168, B: Glu198, B: His201, B: Mn402, B: Hoh501, conact list: Atom Atom Distance (A) Mn OD1 B:Asp66 4.48 Mn NE2 B:Gln69 4.90 Mn CG B:Gln69 4.30 Mn CE B:Met74 4.45 Mn OE1 B:Glu97 3.16 Mn OE2 B:Glu97 1.91 Mn CD B:Glu97 2.88 Mn CG B:Glu97 4.25 Mn ND1 B:His101 4.96 Mn CE1 B:His101 4.87 Mn OE1 B:Glu164 2.30 Mn OE2 B:Glu164 2.32 Mn CD B:Glu164 2.65 Mn CG B:Glu164 4.18 Mn CE2 B:Phe168 4.83 Mn N B:Glu198 4.83 Mn OE1 B:Glu198 2.08 Mn CB B:Glu198 4.37 Mn OE2 B:Glu198 3.71 Mn CD B:Glu198 3.15 Mn CG B:Glu198 4.31 Mn CA B:Glu198 4.17 Mn NE2 B:His201 4.37 Mn CB B:His201 3.74 Mn ND1 B:His201 2.33 Mn CD2 B:His201 4.49 Mn CE1 B:His201 3.19 Mn CG B:His201 3.40 Mn MN B:Mn402 3.91 Mn O B:Hoh501 2.37 interactive model: Manganese binding site 4 out of 4 in 4dr0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 4dr0. 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: Asp66, B: Glu97, B: His101, B: Phe168, B: Ile194, B: Glu198, B: Mn401, B: Hoh501, B: Hoh502, B: Hoh591, conact list: Atom Atom Distance (A) Mn CB B:Asp66 4.04 Mn OD2 B:Asp66 2.16 Mn OD1 B:Asp66 2.33 Mn CG B:Asp66 2.55 Mn CA B:Asp66 4.89 Mn N B:Glu97 4.94 Mn OE1 B:Glu97 1.99 Mn CB B:Glu97 4.34 Mn OE2 B:Glu97 3.80 Mn CD B:Glu97 3.17 Mn CG B:Glu97 4.32 Mn CA B:Glu97 4.18 Mn NE2 B:His101 4.22 Mn CB B:His101 3.48 Mn ND1 B:His101 2.15 Mn CD2 B:His101 4.28 Mn CE1 B:His101 3.09 Mn CG B:His101 3.16 Mn CZ B:Phe168 4.96 Mn CG2 B:Ile194 4.50 Mn OE1 B:Glu198 3.20 Mn OE2 B:Glu198 2.08 Mn CD B:Glu198 2.99 Mn CG B:Glu198 4.39 Mn MN B:Mn401 3.91 Mn O B:Hoh501 3.41 Mn O B:Hoh502 3.94 Mn O B:Hoh591 4.46 interactive model: