Manganese in the structure of Crystal Structure Of A Closed Form of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme (pdb 1do8)

The binding sites of Manganese atom in the structure of Crystal Structure Of A Closed Form of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme (pdb code 1do8). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1do8 structure was solved by Z.YANG, D.L.FLOYD, G.LOEBER, L.TONG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.2 Space group C121 a (A) 229.000 b (A) 118.700 c (A) 113.000 alpha (°) 90.00 beta (°) 109.60 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 26.3 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1do8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1do8. 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: Arg165, A: Leu167, A: Lys183, A: Glu255, A: Asp256, A: Asp279, A: Asn467, A: Oxl603, A: Nad601, A: Hoh606, A: Hoh4750, conact list: Atom Atom Distance (A) Mn CZ A:Arg165 4.46 Mn NH2 A:Arg165 3.66 Mn NH1 A:Arg165 4.50 Mn CD2 A:Leu167 4.84 Mn CE A:Lys183 4.56 Mn NZ A:Lys183 4.39 Mn OE1 A:Glu255 2.43 Mn OE2 A:Glu255 4.60 Mn CD A:Glu255 3.50 Mn CG A:Glu255 3.89 Mn N A:Asp256 4.23 Mn CB A:Asp256 4.52 Mn OD2 A:Asp256 3.72 Mn OD1 A:Asp256 2.19 Mn CG A:Asp256 3.28 Mn CA A:Asp256 4.67 Mn CB A:Asp279 4.54 Mn OD2 A:Asp279 3.43 Mn OD1 A:Asp279 2.23 Mn CG A:Asp279 3.18 Mn ND2 A:Asn467 4.65 Mn O2 A:Oxl603 4.22 Mn C1 A:Oxl603 3.10 Mn O1 A:Oxl603 2.43 Mn O3 A:Oxl603 4.30 Mn O4 A:Oxl603 2.30 Mn C2 A:Oxl603 3.04 Mn C5N A:Nad601 4.56 Mn O A:Hoh606 2.36 Mn O A:Hoh4750 4.50 interactive model: Manganese binding site 2 out of 4 in 1do8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1do8. 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: Arg1165, B: Lys1183, B: Glu1255, B: Asp1256, B: Asp1278, B: Asp1279, B: Asn1467, B: Oxl1603, B: Nad1601, B: Hoh1606, B: Hoh4687, conact list: Atom Atom Distance (A) Mn CZ B:Arg1165 4.48 Mn NH2 B:Arg1165 3.56 Mn NH1 B:Arg1165 4.55 Mn CE B:Lys1183 4.38 Mn NZ B:Lys1183 4.22 Mn OE1 B:Glu1255 2.28 Mn CB B:Glu1255 4.79 Mn OE2 B:Glu1255 4.39 Mn CD B:Glu1255 3.23 Mn C B:Glu1255 4.99 Mn CG B:Glu1255 3.46 Mn N B:Asp1256 4.20 Mn CB B:Asp1256 4.52 Mn OD2 B:Asp1256 3.96 Mn OD1 B:Asp1256 2.23 Mn CG B:Asp1256 3.38 Mn CA B:Asp1256 4.64 Mn OD2 B:Asp1278 4.89 Mn CB B:Asp1279 4.58 Mn OD2 B:Asp1279 3.54 Mn OD1 B:Asp1279 2.29 Mn CG B:Asp1279 3.25 Mn ND2 B:Asn1467 4.76 Mn O2 B:Oxl1603 4.35 Mn C1 B:Oxl1603 3.09 Mn O1 B:Oxl1603 2.36 Mn O3 B:Oxl1603 4.25 Mn O4 B:Oxl1603 2.57 Mn C2 B:Oxl1603 3.17 Mn C5N B:Nad1601 4.76 Mn O B:Hoh1606 2.39 Mn O B:Hoh4687 4.82 interactive model: Manganese binding site 3 out of 4 in 1do8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1do8. 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: Arg2165, C: Lys2183, C: Glu2255, C: Asp2256, C: Asp2278, C: Asp2279, C: Asn2467, C: Oxl2603, C: Nad2601, C: Hoh2606, conact list: Atom Atom Distance (A) Mn CZ C:Arg2165 4.57 Mn NH2 C:Arg2165 3.67 Mn NH1 C:Arg2165 4.64 Mn NZ C:Lys2183 3.90 Mn OE1 C:Glu2255 2.30 Mn OE2 C:Glu2255 4.47 Mn CD C:Glu2255 3.37 Mn CG C:Glu2255 3.79 Mn N C:Asp2256 4.29 Mn CB C:Asp2256 4.48 Mn OD2 C:Asp2256 3.63 Mn OD1 C:Asp2256 2.23 Mn CG C:Asp2256 3.23 Mn CA C:Asp2256 4.67 Mn OD2 C:Asp2278 4.99 Mn CB C:Asp2279 4.50 Mn OD2 C:Asp2279 3.57 Mn OD1 C:Asp2279 2.18 Mn CG C:Asp2279 3.20 Mn CA C:Asp2279 4.97 Mn ND2 C:Asn2467 4.66 Mn O2 C:Oxl2603 4.20 Mn C1 C:Oxl2603 2.94 Mn O1 C:Oxl2603 2.21 Mn O3 C:Oxl2603 4.11 Mn O4 C:Oxl2603 2.41 Mn C2 C:Oxl2603 3.02 Mn C5N C:Nad2601 4.53 Mn O C:Hoh2606 2.55 interactive model: Manganese binding site 4 out of 4 in 1do8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1do8. 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: Arg3165, D: Leu3167, D: Lys3183, D: Glu3255, D: Asp3256, D: Asp3279, D: Asn3467, D: Oxl3603, D: Nad3601, D: Hoh3606, D: Hoh4349, conact list: Atom Atom Distance (A) Mn CZ D:Arg3165 4.39 Mn NH2 D:Arg3165 3.56 Mn NH1 D:Arg3165 4.43 Mn CD2 D:Leu3167 4.95 Mn CE D:Lys3183 4.71 Mn NZ D:Lys3183 4.34 Mn OE1 D:Glu3255 2.27 Mn CB D:Glu3255 4.98 Mn OE2 D:Glu3255 4.39 Mn CD D:Glu3255 3.31 Mn CG D:Glu3255 3.73 Mn N D:Asp3256 4.20 Mn CB D:Asp3256 4.45 Mn OD2 D:Asp3256 3.60 Mn OD1 D:Asp3256 2.25 Mn CG D:Asp3256 3.22 Mn CA D:Asp3256 4.63 Mn CB D:Asp3279 4.56 Mn OD2 D:Asp3279 3.69 Mn OD1 D:Asp3279 2.20 Mn CG D:Asp3279 3.28 Mn ND2 D:Asn3467 4.72 Mn O2 D:Oxl3603 4.22 Mn C1 D:Oxl3603 3.03 Mn O1 D:Oxl3603 2.34 Mn O3 D:Oxl3603 4.21 Mn O4 D:Oxl3603 2.37 Mn C2 D:Oxl3603 3.04 Mn C5N D:Nad3601 4.51 Mn O D:Hoh3606 2.44 Mn O D:Hoh4349 4.78 interactive model: