Manganese in the structure of Crystal Structures of D-Psicose 3-Epimerase From Clostridium Cellulolyticum H10 and Its Complex With Ketohexose Sugars (pdb 3vni)

The binding sites of Manganese atom in the structure of Crystal Structures of D-Psicose 3-Epimerase From Clostridium Cellulolyticum H10 and Its Complex With Ketohexose Sugars (pdb code 3vni). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3vni structure was solved by H.C.CHAN, Y.ZHU, Y.HU, T.P.KO, C.H.HUANG, F.REN, C.C.CHEN, R.T.GUO, Y.SUN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.0 Space group P1211 a (A) 79.761 b (A) 115.441 c (A) 91.627 alpha (°) 90.00 beta (°) 105.45 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 22 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3vni Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3vni. 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: Glu150, A: Asp183, A: His186, A: His209, A: Arg215, A: Glu244, A: Hoh7170, A: Hoh7174, A: Hoh7306, conact list: Atom Atom Distance (A) Mn OE1 A:Glu150 3.36 Mn OE2 A:Glu150 2.18 Mn CD A:Glu150 3.12 Mn CG A:Glu150 4.54 Mn CB A:Asp183 3.94 Mn OD2 A:Asp183 2.20 Mn OD1 A:Asp183 4.36 Mn CG A:Asp183 3.35 Mn NE2 A:His186 4.44 Mn CD2 A:His186 4.45 Mn NE2 A:His209 4.73 Mn CB A:His209 3.58 Mn ND1 A:His209 2.62 Mn CD2 A:His209 4.67 Mn CE1 A:His209 3.65 Mn CG A:His209 3.47 Mn NH1 A:Arg215 4.81 Mn OE1 A:Glu244 2.43 Mn CB A:Glu244 4.83 Mn OE2 A:Glu244 3.28 Mn CD A:Glu244 3.17 Mn CG A:Glu244 4.56 Mn O A:Hoh7170 4.64 Mn O A:Hoh7174 4.66 Mn O A:Hoh7306 2.44 interactive model: Manganese binding site 2 out of 4 in 3vni Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3vni. 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: Glu150, B: Met181, B: Asp183, B: His186, B: His209, B: Arg215, B: Glu244, B: Hoh473, B: Hoh499, B: Hoh615, conact list: Atom Atom Distance (A) Mn OE1 B:Glu150 3.34 Mn OE2 B:Glu150 2.01 Mn CD B:Glu150 3.00 Mn CG B:Glu150 4.37 Mn CE B:Met181 4.26 Mn CB B:Asp183 3.86 Mn OD2 B:Asp183 2.26 Mn OD1 B:Asp183 4.41 Mn CG B:Asp183 3.36 Mn NE2 B:His186 4.58 Mn CD2 B:His186 4.46 Mn NE2 B:His209 4.53 Mn CB B:His209 3.58 Mn ND1 B:His209 2.43 Mn CD2 B:His209 4.54 Mn CE1 B:His209 3.41 Mn CG B:His209 3.37 Mn NH1 B:Arg215 4.83 Mn OE1 B:Glu244 2.32 Mn CB B:Glu244 4.94 Mn OE2 B:Glu244 3.48 Mn CD B:Glu244 3.26 Mn CG B:Glu244 4.65 Mn O B:Hoh473 4.32 Mn O B:Hoh499 4.94 Mn O B:Hoh615 4.83 interactive model: Manganese binding site 3 out of 4 in 3vni Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3vni. 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: Glu150, C: Met181, C: Asp183, C: His186, C: His209, C: Arg215, C: Glu244, C: Hoh416, C: Hoh482, C: Hoh512, conact list: Atom Atom Distance (A) Mn OE1 C:Glu150 3.80 Mn OE2 C:Glu150 2.13 Mn CD C:Glu150 3.27 Mn CG C:Glu150 4.48 Mn CE C:Met181 4.57 Mn CB C:Asp183 3.92 Mn OD2 C:Asp183 2.25 Mn OD1 C:Asp183 4.40 Mn CG C:Asp183 3.38 Mn NE2 C:His186 4.43 Mn CD2 C:His186 4.42 Mn NE2 C:His209 4.66 Mn CB C:His209 3.58 Mn ND1 C:His209 2.55 Mn CD2 C:His209 4.62 Mn CE1 C:His209 3.56 Mn CG C:His209 3.44 Mn NH1 C:Arg215 4.96 Mn OE1 C:Glu244 2.46 Mn CB C:Glu244 4.87 Mn OE2 C:Glu244 3.49 Mn CD C:Glu244 3.28 Mn CG C:Glu244 4.62 Mn O C:Hoh416 4.91 Mn O C:Hoh482 4.83 Mn O C:Hoh512 4.62 interactive model: Manganese binding site 4 out of 4 in 3vni Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3vni. 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: Glu150, D: Met181, D: Asp183, D: His186, D: His209, D: Arg215, D: Glu244, D: Hoh433, D: Hoh439, D: Hoh553, D: Hoh636, D: Hoh637, conact list: Atom Atom Distance (A) Mn OE1 D:Glu150 3.27 Mn OE2 D:Glu150 2.05 Mn CD D:Glu150 2.99 Mn CG D:Glu150 4.40 Mn CE D:Met181 4.16 Mn CB D:Asp183 3.90 Mn OD2 D:Asp183 2.26 Mn OD1 D:Asp183 4.43 Mn CG D:Asp183 3.38 Mn NE2 D:His186 4.48 Mn CD2 D:His186 4.52 Mn NE2 D:His209 4.62 Mn CB D:His209 3.71 Mn ND1 D:His209 2.54 Mn CD2 D:His209 4.65 Mn CE1 D:His209 3.49 Mn CG D:His209 3.50 Mn NH1 D:Arg215 4.88 Mn OE1 D:Glu244 2.38 Mn CB D:Glu244 4.85 Mn OE2 D:Glu244 3.47 Mn CD D:Glu244 3.23 Mn CG D:Glu244 4.57 Mn O D:Hoh433 4.94 Mn O D:Hoh439 4.50 Mn O D:Hoh553 4.80 Mn O D:Hoh636 2.54 Mn O D:Hoh637 2.74 interactive model: