Manganese in the structure of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift (pdb 1s5m)

The binding sites of Manganese atom in the structure of Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of A Metal-Mediated Hydride Shift (pdb code 1s5m). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1s5m structure was solved by T.D.FENN, D.RINGE, G.A.PETSKO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.0 Space group I222 a (A) 85.865 b (A) 92.968 c (A) 98.298 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 11.1 Rfree (%) 12.9 Manganese Binding Sites: Manganese binding site 1 out of 2 in 1s5m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1s5m. 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: Trp15, A: Glu180, A: Asn214, A: Glu216, A: His219, A: Asp244, A: Asp286, A: Glc1001, A: Mn2002, A: Hoh2078, A: Hoh2416, conact list: Atom Atom Distance (A) Mn HZ2 A:Trp15 4.73 Mn OE1 A:Glu180 3.34 Mn HG3 A:Glu180 4.57 Mn OE2 A:Glu180 2.10 Mn CD A:Glu180 3.04 Mn CG A:Glu180 4.37 Mn HG2 A:Glu180 4.63 Mn HD21 A:Asn214 4.67 Mn HD22 A:Asn214 4.89 Mn HB2 A:Glu216 3.33 Mn OE1 A:Glu216 2.04 Mn HG3 A:Glu216 4.00 Mn CB A:Glu216 4.05 Mn HB3 A:Glu216 4.35 Mn OE2 A:Glu216 4.22 Mn CD A:Glu216 3.24 Mn CG A:Glu216 3.97 Mn HG2 A:Glu216 4.91 Mn HD1 A:His219 4.76 Mn NE2 A:His219 4.53 Mn HE1 A:His219 3.50 Mn ND1 A:His219 4.64 Mn CE1 A:His219 3.97 Mn HB2 A:Asp244 3.95 Mn CB A:Asp244 3.97 Mn HB3 A:Asp244 3.75 Mn OD2 A:Asp244 2.15 Mn OD1 A:Asp244 4.32 Mn CG A:Asp244 3.33 Mn HB2 A:Asp286 3.57 Mn HB2 A:Asp286 3.76 Mn CB A:Asp286 3.59 Mn CB A:Asp286 3.65 Mn HB3 A:Asp286 3.36 Mn HB3 A:Asp286 3.31 Mn OD2 A:Asp286 2.13 Mn OD2 A:Asp286 2.17 Mn OD1 A:Asp286 4.30 Mn OD1 A:Asp286 4.10 Mn CG A:Asp286 3.18 Mn CG A:Asp286 3.11 Mn H5 A:Glc1001 4.52 Mn HO4 A:Glc1001 1.60 Mn HO2 A:Glc1001 4.79 Mn O3 A:Glc1001 2.40 Mn C2 A:Glc1001 4.57 Mn H3 A:Glc1001 3.23 Mn C6 A:Glc1001 4.88 Mn H62 A:Glc1001 4.34 Mn C5 A:Glc1001 4.43 Mn HO3 A:Glc1001 1.95 Mn H2 A:Glc1001 4.81 Mn C4 A:Glc1001 3.11 Mn H4 A:Glc1001 3.49 Mn C3 A:Glc1001 3.12 Mn O4 A:Glc1001 2.25 Mn MN A:Mn2002 4.57 Mn O A:Hoh2078 4.06 Mn O A:Hoh2416 3.71 interactive model: Manganese binding site 2 out of 2 in 1s5m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1s5m. 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: Lys182, A: Glu216, A: Gly218, A: His219, A: Asn246, A: Asp254, A: Asp256, A: Asp286, A: Glc1001, A: Mn2001, A: Hoh2026, A: Hoh2138, A: Hoh2306, A: Hoh2416, conact list: Atom Atom Distance (A) Mn HZ3 A:Lys182 4.51 Mn HE3 A:Lys182 4.00 Mn HD2 A:Lys182 4.91 Mn CE A:Lys182 4.84 Mn NZ A:Lys182 4.98 Mn HZ1 A:Lys182 4.93 Mn OE1 A:Glu216 3.03 Mn HG3 A:Glu216 4.84 Mn OE2 A:Glu216 2.05 Mn CD A:Glu216 2.90 Mn CG A:Glu216 4.30 Mn HG2 A:Glu216 4.45 Mn HA3 A:Gly218 4.93 Mn CD2 A:His219 3.06 Mn CG A:His219 4.24 Mn HD2 A:His219 3.12 Mn NE2 A:His219 2.31 Mn HE1 A:His219 3.62 Mn ND1 A:His219 4.36 Mn CE1 A:His219 3.33 Mn HD21 A:Asn246 3.35 Mn HD22 A:Asn246 4.00 Mn ND2 A:Asn246 4.01 Mn HB2 A:Asp254 4.44 Mn CB A:Asp254 4.08 Mn HB3 A:Asp254 4.48 Mn HA A:Asp254 4.96 Mn OD2 A:Asp254 2.22 Mn OD1 A:Asp254 2.30 Mn CG A:Asp254 2.60 Mn CA A:Asp254 5.00 Mn N A:Asp256 4.95 Mn CB A:Asp256 4.54 Mn HA A:Asp256 4.55 Mn OD2 A:Asp256 3.40 Mn H A:Asp256 4.60 Mn OD1 A:Asp256 2.20 Mn CG A:Asp256 3.14 Mn CA A:Asp256 4.94 Mn OD2 A:Asp286 4.24 Mn HO2 A:Glc1001 4.51 Mn O3 A:Glc1001 4.00 Mn HO3 A:Glc1001 4.33 Mn MN A:Mn2001 4.57 Mn O A:Hoh2026 3.97 Mn O A:Hoh2138 3.67 Mn O A:Hoh2306 4.88 Mn O A:Hoh2416 2.16 interactive model: