Manganese in the structure of Arginase From Bacillus Caldevelox, Complexed With L-Arginine (pdb 3cev)

The binding sites of Manganese atom in the structure of Arginase From Bacillus Caldevelox, Complexed With L-Arginine (pdb code 3cev). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3cev structure was solved by M.C.BEWLEY, P.D.JEFFREY, M.L.PATCHETT, Z.F.KANYO, E.N.BAKER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.4 Space group C2221 a (A) 106.800 b (A) 277.700 c (A) 140.000 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 24.3 Manganese Binding Sites: Manganese binding site 1 out of 6 in 3cev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3cev. 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: His99, A: Trp120, A: Asp122, A: Asp126, A: His139, A: Asp226, A: Asp228, A: Glu271, A: Arg407, A: Hoh408, A: Hoh455, conact list: Atom Atom Distance (A) Mn NE2 A:His99 4.29 Mn CB A:His99 3.63 Mn ND1 A:His99 2.24 Mn CD2 A:His99 4.38 Mn CE1 A:His99 3.14 Mn CG A:His99 3.28 Mn CZ2 A:Trp120 4.97 Mn CE2 A:Trp120 4.92 Mn NE1 A:Trp120 4.24 Mn CB A:Asp122 4.41 Mn OD2 A:Asp122 2.15 Mn OD1 A:Asp122 3.21 Mn CG A:Asp122 3.02 Mn CB A:Asp126 4.63 Mn OD2 A:Asp126 2.27 Mn OD1 A:Asp126 3.58 Mn CG A:Asp126 3.28 Mn O A:His139 4.59 Mn CB A:Asp226 3.53 Mn OD2 A:Asp226 2.19 Mn OD1 A:Asp226 4.31 Mn CG A:Asp226 3.19 Mn CA A:Asp226 4.96 Mn OD2 A:Asp228 4.45 Mn OD1 A:Asp228 4.73 Mn CG A:Asp228 4.95 Mn OE2 A:Glu271 4.73 Mn CG A:Glu271 4.93 Mn CZ A:Arg407 3.24 Mn NE A:Arg407 3.90 Mn NH2 A:Arg407 2.54 Mn NH1 A:Arg407 3.88 Mn O A:Hoh408 2.24 Mn O A:Hoh455 4.89 interactive model: Manganese binding site 2 out of 6 in 3cev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3cev. 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: His99, B: Trp120, B: Asp122, B: Asp126, B: His139, B: Asp226, B: Asp228, B: Glu271, B: Arg408, B: Hoh409, conact list: Atom Atom Distance (A) Mn NE2 B:His99 4.27 Mn CB B:His99 3.64 Mn ND1 B:His99 2.23 Mn CD2 B:His99 4.37 Mn CE1 B:His99 3.11 Mn CG B:His99 3.28 Mn CZ2 B:Trp120 4.89 Mn CE2 B:Trp120 4.87 Mn NE1 B:Trp120 4.19 Mn CB B:Asp122 4.39 Mn OD2 B:Asp122 2.12 Mn OD1 B:Asp122 3.21 Mn CG B:Asp122 3.01 Mn CB B:Asp126 4.62 Mn OD2 B:Asp126 2.27 Mn OD1 B:Asp126 3.55 Mn CG B:Asp126 3.27 Mn O B:His139 4.61 Mn CB B:Asp226 3.53 Mn OD2 B:Asp226 2.17 Mn OD1 B:Asp226 4.31 Mn CG B:Asp226 3.18 Mn CA B:Asp226 4.97 Mn OD2 B:Asp228 4.34 Mn OD1 B:Asp228 4.74 Mn CG B:Asp228 4.91 Mn OE2 B:Glu271 4.92 Mn CG B:Glu271 4.96 Mn CZ B:Arg408 3.25 Mn NE B:Arg408 3.93 Mn NH2 B:Arg408 2.53 Mn NH1 B:Arg408 3.87 Mn O B:Hoh409 2.27 interactive model: Manganese binding site 3 out of 6 in 3cev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3cev. 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: His99, C: Trp120, C: Asp122, C: Asp126, C: His139, C: Asp226, C: Asp228, C: Glu271, C: Arg409, C: Hoh410, C: Hoh456, conact list: Atom Atom Distance (A) Mn NE2 C:His99 4.29 Mn CB C:His99 3.58 Mn ND1 C:His99 2.23 Mn CD2 C:His99 4.36 Mn CE1 C:His99 3.15 Mn CG C:His99 3.25 Mn CZ2 C:Trp120 4.90 Mn CE2 C:Trp120 4.88 Mn NE1 C:Trp120 4.22 Mn CB C:Asp122 4.42 Mn OD2 C:Asp122 2.14 Mn OD1 C:Asp122 3.26 Mn CG C:Asp122 3.05 Mn CB C:Asp126 4.62 Mn OD2 C:Asp126 2.26 Mn OD1 C:Asp126 3.57 Mn CG C:Asp126 3.26 Mn O C:His139 4.55 Mn CB C:Asp226 3.56 Mn OD2 C:Asp226 2.16 Mn OD1 C:Asp226 4.31 Mn CG C:Asp226 3.19 Mn CA C:Asp226 4.98 Mn OD2 C:Asp228 4.51 Mn OD1 C:Asp228 4.74 Mn CG C:Asp228 4.98 Mn OE2 C:Glu271 4.83 Mn CG C:Glu271 4.93 Mn CZ C:Arg409 3.28 Mn NE C:Arg409 3.92 Mn NH2 C:Arg409 2.58 Mn NH1 C:Arg409 3.93 Mn O C:Hoh410 2.25 Mn O C:Hoh456 4.99 interactive model: Manganese binding site 4 out of 6 in 3cev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3cev. 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: His99, D: Trp120, D: Asp122, D: Asp126, D: His139, D: Asp226, D: Asp228, D: Glu271, D: Arg410, D: Hoh411, D: Hoh457, conact list: Atom Atom Distance (A) Mn NE2 D:His99 4.28 Mn CB D:His99 3.59 Mn ND1 D:His99 2.22 Mn CD2 D:His99 4.36 Mn CE1 D:His99 3.13 Mn CG D:His99 3.26 Mn CZ2 D:Trp120 4.88 Mn CE2 D:Trp120 4.85 Mn NE1 D:Trp120 4.16 Mn CB D:Asp122 4.42 Mn OD2 D:Asp122 2.13 Mn OD1 D:Asp122 3.26 Mn CG D:Asp122 3.04 Mn CB D:Asp126 4.61 Mn OD2 D:Asp126 2.25 Mn OD1 D:Asp126 3.54 Mn CG D:Asp126 3.25 Mn O D:His139 4.57 Mn CB D:Asp226 3.57 Mn OD2 D:Asp226 2.17 Mn OD1 D:Asp226 4.32 Mn CG D:Asp226 3.20 Mn CA D:Asp226 4.96 Mn OD2 D:Asp228 4.46 Mn OD1 D:Asp228 4.74 Mn CG D:Asp228 4.95 Mn OE2 D:Glu271 4.88 Mn CG D:Glu271 4.98 Mn CZ D:Arg410 3.23 Mn NE D:Arg410 3.91 Mn NH2 D:Arg410 2.51 Mn NH1 D:Arg410 3.86 Mn O D:Hoh411 2.26 Mn O D:Hoh457 4.93 interactive model: Manganese binding site 5 out of 6 in 3cev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 3cev. 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: E: His99, E: Trp120, E: Asp122, E: Asp126, E: His139, E: Asp226, E: Asp228, E: Glu271, E: Arg411, E: Hoh412, conact list: Atom Atom Distance (A) Mn NE2 E:His99 4.29 Mn CB E:His99 3.63 Mn ND1 E:His99 2.25 Mn CD2 E:His99 4.37 Mn CE1 E:His99 3.15 Mn CG E:His99 3.28 Mn CZ2 E:Trp120 4.95 Mn CE2 E:Trp120 4.93 Mn NE1 E:Trp120 4.24 Mn CB E:Asp122 4.40 Mn OD2 E:Asp122 2.13 Mn OD1 E:Asp122 3.19 Mn CG E:Asp122 3.01 Mn CB E:Asp126 4.64 Mn OD2 E:Asp126 2.28 Mn OD1 E:Asp126 3.59 Mn CG E:Asp126 3.29 Mn O E:His139 4.65 Mn CB E:Asp226 3.53 Mn OD2 E:Asp226 2.16 Mn OD1 E:Asp226 4.26 Mn CG E:Asp226 3.15 Mn CA E:Asp226 4.96 Mn OD2 E:Asp228 4.42 Mn OD1 E:Asp228 4.65 Mn CG E:Asp228 4.91 Mn OE2 E:Glu271 4.83 Mn CG E:Glu271 4.92 Mn CZ E:Arg411 3.21 Mn NE E:Arg411 3.86 Mn NH2 E:Arg411 2.45 Mn NH1 E:Arg411 3.89 Mn O E:Hoh412 2.26 interactive model: Manganese binding site 6 out of 6 in 3cev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 3cev. 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: F: His99, F: Trp120, F: Asp122, F: Asp126, F: His139, F: Asp226, F: Asp228, F: Glu271, F: Arg412, F: Hoh413, conact list: Atom Atom Distance (A) Mn NE2 F:His99 4.26 Mn CB F:His99 3.59 Mn ND1 F:His99 2.22 Mn CD2 F:His99 4.34 Mn CE1 F:His99 3.12 Mn CG F:His99 3.24 Mn CZ2 F:Trp120 4.91 Mn CE2 F:Trp120 4.89 Mn NE1 F:Trp120 4.22 Mn CB F:Asp122 4.48 Mn OD2 F:Asp122 2.16 Mn OD1 F:Asp122 3.32 Mn CG F:Asp122 3.09 Mn CB F:Asp126 4.61 Mn OD2 F:Asp126 2.25 Mn OD1 F:Asp126 3.56 Mn CG F:Asp126 3.26 Mn O F:His139 4.53 Mn CB F:Asp226 3.58 Mn OD2 F:Asp226 2.18 Mn OD1 F:Asp226 4.30 Mn CG F:Asp226 3.19 Mn CA F:Asp226 4.97 Mn OD2 F:Asp228 4.45 Mn OD1 F:Asp228 4.73 Mn CG F:Asp228 4.96 Mn OE2 F:Glu271 4.74 Mn CG F:Glu271 4.95 Mn CZ F:Arg412 3.20 Mn NE F:Arg412 3.85 Mn NH2 F:Arg412 2.52 Mn NH1 F:Arg412 3.85 Mn O F:Hoh413 2.25 interactive model: