Manganese in the structure of Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria (pdb 1lwd)

The binding sites of Manganese atom in the structure of Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria (pdb code 1lwd). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1lwd structure was solved by C.CECCARELLI, B.J.BAHNSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.2-1.9 Space group C121 a (A) 137.860 b (A) 112.569 c (A) 66.080 alpha (°) 90.00 beta (°) 97.00 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 21 Manganese Binding Sites: Manganese binding site 1 out of 2 in 1lwd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1lwd. 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: Arg110, A: Arg133, A: Asp275, A: Asp279, B: Lys212, B: Asp252, A: Ict701, A: Hoh1001, A: Hoh1003, A: Hoh1005, B: Hoh1007, conact list: Atom Atom Distance (A) Mn NH1 A:Arg110 4.29 Mn NH1 A:Arg133 4.66 Mn O A:Asp275 4.01 Mn CB A:Asp275 4.39 Mn OD2 A:Asp275 3.76 Mn C A:Asp275 4.50 Mn OD1 A:Asp275 2.06 Mn CG A:Asp275 3.21 Mn CA A:Asp275 4.51 Mn OD2 A:Asp279 4.19 Mn OD1 A:Asp279 4.18 Mn CG A:Asp279 4.42 Mn NZ B:Lys212 4.07 Mn CB B:Asp252 3.70 Mn OD2 B:Asp252 2.29 Mn OD1 B:Asp252 4.41 Mn CG B:Asp252 3.32 Mn C6 A:Ict701 4.24 Mn O5 A:Ict701 4.47 Mn O2 A:Ict701 2.32 Mn C1 A:Ict701 3.04 Mn O1 A:Ict701 4.33 Mn C3 A:Ict701 4.27 Mn O7 A:Ict701 2.23 Mn O6 A:Ict701 4.56 Mn C2 A:Ict701 3.19 Mn O A:Hoh1001 2.17 Mn O A:Hoh1003 2.24 Mn O A:Hoh1005 4.26 Mn O B:Hoh1007 4.98 interactive model: Manganese binding site 2 out of 2 in 1lwd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1lwd. 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: Lys212, A: Asp252, B: Arg110, B: Arg133, B: Asp275, B: Asp279, B: Ict702, A: Hoh1008, B: Hoh1002, B: Hoh1004, B: Hoh1006, B: Hoh1448, conact list: Atom Atom Distance (A) Mn NZ A:Lys212 4.10 Mn CB A:Asp252 3.64 Mn OD2 A:Asp252 2.26 Mn OD1 A:Asp252 4.38 Mn CG A:Asp252 3.28 Mn NH1 B:Arg110 4.36 Mn NH1 B:Arg133 4.68 Mn O B:Asp275 4.01 Mn CB B:Asp275 4.39 Mn OD2 B:Asp275 3.73 Mn C B:Asp275 4.52 Mn OD1 B:Asp275 2.08 Mn CG B:Asp275 3.20 Mn CA B:Asp275 4.53 Mn OD2 B:Asp279 4.18 Mn OD1 B:Asp279 4.21 Mn CG B:Asp279 4.43 Mn C6 B:Ict702 4.20 Mn O5 B:Ict702 4.42 Mn O2 B:Ict702 2.30 Mn C1 B:Ict702 3.02 Mn O1 B:Ict702 4.30 Mn C3 B:Ict702 4.23 Mn O7 B:Ict702 2.20 Mn O6 B:Ict702 4.53 Mn C2 B:Ict702 3.16 Mn O A:Hoh1008 4.89 Mn O B:Hoh1002 2.22 Mn O B:Hoh1004 2.36 Mn O B:Hoh1006 4.08 Mn O B:Hoh1448 4.62 interactive model: