Manganese in the structure of Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199 (pdb 3c5m)

The binding sites of Manganese atom in the structure of Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199 (pdb code 3c5m). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3c5m structure was solved by F.FOROUHAR, M.ABASHIDZE, J.SEETHARAMAN, H.JANJUA, L.MAO, R.XIAO, L.A.OWENS, D.WANG, M.C.BARAN, T.B.ACTON, G.T.MONTELIONE, J.F.HUNT, L.TONG, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM(NESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.6 Space group P321 a (A) 115.233 b (A) 115.233 c (A) 209.950 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.4 Rfree (%) 27.7 Manganese Binding Sites: Manganese binding site 1 out of 3 in 3c5m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3c5m. 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: Phe38, A: His287, A: Gln350, A: His353, A: His355, A: Hoh473, A: Hoh477, conact list: Atom Atom Distance (A) Mn CE2 A:Phe38 4.84 Mn NE2 A:His287 2.01 Mn ND1 A:His287 4.07 Mn CD2 A:His287 2.79 Mn CE1 A:His287 3.08 Mn CG A:His287 3.96 Mn NE2 A:Gln350 3.55 Mn OE1 A:Gln350 2.29 Mn CD A:Gln350 3.25 Mn CG A:Gln350 4.66 Mn NE2 A:His353 4.26 Mn CB A:His353 3.65 Mn ND1 A:His353 2.21 Mn CD2 A:His353 4.37 Mn CE1 A:His353 3.09 Mn CG A:His353 3.28 Mn NE2 A:His355 2.16 Mn ND1 A:His355 4.30 Mn CD2 A:His355 3.01 Mn CE1 A:His355 3.25 Mn CG A:His355 4.22 Mn O A:Hoh473 3.14 Mn O A:Hoh477 2.26 interactive model: Manganese binding site 2 out of 3 in 3c5m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3c5m. 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: Phe38, B: His287, B: Gln350, B: His353, B: His355, B: Hoh402, conact list: Atom Atom Distance (A) Mn CE2 B:Phe38 4.91 Mn NE2 B:His287 2.02 Mn ND1 B:His287 4.11 Mn CD2 B:His287 2.79 Mn CE1 B:His287 3.12 Mn CG B:His287 3.99 Mn NE2 B:Gln350 3.41 Mn OE1 B:Gln350 2.18 Mn CD B:Gln350 3.12 Mn CG B:Gln350 4.55 Mn NE2 B:His353 4.25 Mn CB B:His353 3.74 Mn ND1 B:His353 2.24 Mn CD2 B:His353 4.40 Mn CE1 B:His353 3.07 Mn CG B:His353 3.34 Mn NE2 B:His355 2.26 Mn ND1 B:His355 4.38 Mn CD2 B:His355 3.15 Mn CE1 B:His355 3.30 Mn CG B:His355 4.34 Mn O B:Hoh402 2.60 interactive model: Manganese binding site 3 out of 3 in 3c5m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3c5m. 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: Phe38, C: His287, C: Gln350, C: His353, C: His355, C: Hoh417, C: Hoh452, conact list: Atom Atom Distance (A) Mn CE2 C:Phe38 4.97 Mn NE2 C:His287 2.08 Mn ND1 C:His287 4.19 Mn CD2 C:His287 2.85 Mn CE1 C:His287 3.19 Mn CG C:His287 4.06 Mn NE2 C:Gln350 3.33 Mn OE1 C:Gln350 2.30 Mn CD C:Gln350 3.16 Mn CG C:Gln350 4.62 Mn NE2 C:His353 4.22 Mn CB C:His353 3.93 Mn ND1 C:His353 2.27 Mn CD2 C:His353 4.45 Mn CE1 C:His353 3.00 Mn CG C:His353 3.44 Mn NE2 C:His355 2.49 Mn ND1 C:His355 4.62 Mn CD2 C:His355 3.34 Mn CE1 C:His355 3.55 Mn CG C:His355 4.56 Mn O C:Hoh417 3.06 Mn O C:Hoh452 2.59 interactive model: