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 |
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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 |
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| 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 |
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