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 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: