Manganese in the structure of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii With D-Tagatose (pdb 2qum)
The binding sites of Manganese atom in the structure of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii With D-Tagatose (pdb code 2qum). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2qum structure was solved by H.YOSHIDA, M.YAMADA, T.NISHITANI, G.TAKADA, K.IZUMORI, S.KAMITORI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 41.3-2.3 | Space group | P1211 | a (A) | 49.414 | b (A) | 139.432 | c (A) | 92.860 | alpha (°) | 90.00 | beta (°) | 104.04 | gamma (°) | 90.00 | Rfactor (%) | 18.5 | Rfree (%) | 23.9 |
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Manganese Binding Sites:Manganese binding site 1 out of 4 in 2qum
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2qum. 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: Glu152, A: Gln183, A: Asp185, A: His188, A: His211, A: Arg217, A: Glu246, A: Tag291, A: Hoh293, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 A:Glu152 | 3.70 | Mn | OE2 A:Glu152 | 2.32 | Mn | CD A:Glu152 | 3.28 | Mn | CG A:Glu152 | 4.49 | Mn | NE2 A:Gln183 | 4.28 | Mn | CB A:Asp185 | 3.88 | Mn | OD2 A:Asp185 | 2.29 | Mn | OD1 A:Asp185 | 4.46 | Mn | CG A:Asp185 | 3.39 | Mn | NE2 A:His188 | 4.56 | Mn | CD2 A:His188 | 4.40 | Mn | NE2 A:His211 | 4.30 | Mn | CB A:His211 | 3.72 | Mn | ND1 A:His211 | 2.27 | Mn | CD2 A:His211 | 4.43 | Mn | CE1 A:His211 | 3.12 | Mn | CG A:His211 | 3.35 | Mn | NH2 A:Arg217 | 4.11 | Mn | OE1 A:Glu246 | 2.59 | Mn | OE2 A:Glu246 | 3.40 | Mn | CD A:Glu246 | 3.33 | Mn | CG A:Glu246 | 4.73 | Mn | O2 A:Tag291 | 2.33 | Mn | C4 A:Tag291 | 4.81 | Mn | C1 A:Tag291 | 4.44 | Mn | O1 A:Tag291 | 4.96 | Mn | C3 A:Tag291 | 3.27 | Mn | O3 A:Tag291 | 3.00 | Mn | C2 A:Tag291 | 3.08 | Mn | O A:Hoh293 | 4.90 |
| interactive model:
| Manganese binding site 2 out of 4 in 2qum
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2qum. 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: Glu152, B: Gln183, B: Asp185, B: His188, B: His211, B: Arg217, B: Glu246, B: Tag291, B: Hoh308, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 B:Glu152 | 3.80 | Mn | OE2 B:Glu152 | 2.25 | Mn | CD B:Glu152 | 3.35 | Mn | CG B:Glu152 | 4.62 | Mn | NE2 B:Gln183 | 4.24 | Mn | CB B:Asp185 | 3.86 | Mn | OD2 B:Asp185 | 2.29 | Mn | OD1 B:Asp185 | 4.48 | Mn | CG B:Asp185 | 3.39 | Mn | NE2 B:His188 | 4.42 | Mn | CD2 B:His188 | 4.38 | Mn | NE2 B:His211 | 4.22 | Mn | CB B:His211 | 3.53 | Mn | ND1 B:His211 | 2.16 | Mn | CD2 B:His211 | 4.30 | Mn | CE1 B:His211 | 3.08 | Mn | CG B:His211 | 3.19 | Mn | NH2 B:Arg217 | 4.33 | Mn | OE1 B:Glu246 | 2.43 | Mn | CB B:Glu246 | 4.93 | Mn | OE2 B:Glu246 | 3.53 | Mn | CD B:Glu246 | 3.32 | Mn | CG B:Glu246 | 4.68 | Mn | O2 B:Tag291 | 2.37 | Mn | C4 B:Tag291 | 4.67 | Mn | C1 B:Tag291 | 4.39 | Mn | C3 B:Tag291 | 3.12 | Mn | O3 B:Tag291 | 2.83 | Mn | C2 B:Tag291 | 3.00 | Mn | O B:Hoh308 | 4.93 |
| interactive model:
| Manganese binding site 3 out of 4 in 2qum
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2qum. 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: Glu152, C: Gln183, C: Asp185, C: His188, C: His211, C: Arg217, C: Glu246, C: Tag291, C: Hoh357, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 C:Glu152 | 3.85 | Mn | OE2 C:Glu152 | 2.16 | Mn | CD C:Glu152 | 3.32 | Mn | CG C:Glu152 | 4.52 | Mn | NE2 C:Gln183 | 4.28 | Mn | CB C:Asp185 | 3.82 | Mn | OD2 C:Asp185 | 2.06 | Mn | OD1 C:Asp185 | 4.20 | Mn | CG C:Asp185 | 3.20 | Mn | NE2 C:His188 | 4.42 | Mn | CD2 C:His188 | 4.28 | Mn | NE2 C:His211 | 4.35 | Mn | CB C:His211 | 3.56 | Mn | ND1 C:His211 | 2.28 | Mn | CD2 C:His211 | 4.40 | Mn | CE1 C:His211 | 3.22 | Mn | CG C:His211 | 3.27 | Mn | NH2 C:Arg217 | 4.04 | Mn | OE1 C:Glu246 | 2.46 | Mn | CB C:Glu246 | 4.98 | Mn | OE2 C:Glu246 | 3.60 | Mn | CD C:Glu246 | 3.37 | Mn | CG C:Glu246 | 4.73 | Mn | O2 C:Tag291 | 2.19 | Mn | C4 C:Tag291 | 4.78 | Mn | C1 C:Tag291 | 4.29 | Mn | O1 C:Tag291 | 4.85 | Mn | C3 C:Tag291 | 3.23 | Mn | O3 C:Tag291 | 3.14 | Mn | C2 C:Tag291 | 2.95 | Mn | O C:Hoh357 | 4.02 |
| interactive model:
| Manganese binding site 4 out of 4 in 2qum
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2qum. 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: Glu152, D: Gln183, D: Asp185, D: His188, D: His211, D: Arg217, D: Glu246, D: Tag291, D: Hoh306, D: Hoh423, | conact list:
Atom | Atom | Distance (A) | Mn | OE1 D:Glu152 | 3.69 | Mn | OE2 D:Glu152 | 2.37 | Mn | CD D:Glu152 | 3.38 | Mn | CG D:Glu152 | 4.72 | Mn | NE2 D:Gln183 | 4.40 | Mn | CB D:Asp185 | 3.93 | Mn | OD2 D:Asp185 | 2.10 | Mn | OD1 D:Asp185 | 4.24 | Mn | CG D:Asp185 | 3.27 | Mn | NE2 D:His188 | 4.39 | Mn | CD2 D:His188 | 4.33 | Mn | NE2 D:His211 | 4.43 | Mn | CB D:His211 | 3.55 | Mn | ND1 D:His211 | 2.34 | Mn | CD2 D:His211 | 4.46 | Mn | CE1 D:His211 | 3.31 | Mn | CG D:His211 | 3.31 | Mn | NH2 D:Arg217 | 4.72 | Mn | OE1 D:Glu246 | 2.39 | Mn | CB D:Glu246 | 4.87 | Mn | OE2 D:Glu246 | 3.42 | Mn | CD D:Glu246 | 3.23 | Mn | CG D:Glu246 | 4.60 | Mn | O2 D:Tag291 | 2.24 | Mn | C4 D:Tag291 | 4.91 | Mn | C1 D:Tag291 | 4.39 | Mn | O1 D:Tag291 | 4.86 | Mn | C3 D:Tag291 | 3.37 | Mn | O3 D:Tag291 | 3.00 | Mn | C2 D:Tag291 | 3.07 | Mn | O D:Hoh306 | 4.94 | Mn | O D:Hoh423 | 4.10 |
| interactive model:
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