Manganese in the structure of Molecular Mechanism Of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate (pdb 1gz4)

The binding sites of Manganese atom in the structure of Molecular Mechanism Of the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp and Fumarate (pdb code 1gz4). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1gz4 structure was solved by Z.YANG, C.W.LANKS, 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) 224.944 b (A) 117.454 c (A) 111.610 alpha (°) 90.00 beta (°) 109.33 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 24.5 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1gz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1gz4. 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: Ttn603, A: Hoh2146, A: Hoh2148, conact list: Atom Atom Distance (A) Mn NH2 A:Arg165 3.93 Mn CD2 A:Leu167 4.86 Mn CE A:Lys183 4.48 Mn NZ A:Lys183 4.31 Mn OE1 A:Glu255 2.29 Mn OE2 A:Glu255 4.47 Mn CD A:Glu255 3.39 Mn CG A:Glu255 3.88 Mn N A:Asp256 4.24 Mn CB A:Asp256 4.52 Mn OD2 A:Asp256 3.66 Mn OD1 A:Asp256 2.26 Mn CG A:Asp256 3.28 Mn CA A:Asp256 4.65 Mn CB A:Asp279 4.55 Mn OD2 A:Asp279 3.34 Mn OD1 A:Asp279 2.28 Mn CG A:Asp279 3.16 Mn ND2 A:Asn467 4.76 Mn O5 A:Ttn603 4.58 Mn O2 A:Ttn603 4.27 Mn C1 A:Ttn603 3.09 Mn O1 A:Ttn603 2.38 Mn C3 A:Ttn603 4.37 Mn O3 A:Ttn603 2.23 Mn C2 A:Ttn603 3.13 Mn O A:Hoh2146 4.61 Mn O A:Hoh2148 2.66 interactive model: Manganese binding site 2 out of 4 in 1gz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1gz4. 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: Arg165, B: Leu167, B: Lys183, B: Glu255, B: Asp256, B: Asp279, B: Asn467, B: Ttn603, B: Hoh2071, B: Hoh2138, conact list: Atom Atom Distance (A) Mn CZ B:Arg165 4.85 Mn NH2 B:Arg165 3.66 Mn CD2 B:Leu167 4.91 Mn CE B:Lys183 4.35 Mn NZ B:Lys183 4.17 Mn OE1 B:Glu255 2.41 Mn OE2 B:Glu255 4.61 Mn CD B:Glu255 3.53 Mn CG B:Glu255 4.00 Mn N B:Asp256 4.29 Mn CB B:Asp256 4.57 Mn OD2 B:Asp256 3.77 Mn OD1 B:Asp256 2.24 Mn CG B:Asp256 3.32 Mn CA B:Asp256 4.69 Mn CB B:Asp279 4.58 Mn OD2 B:Asp279 3.32 Mn OD1 B:Asp279 2.30 Mn CG B:Asp279 3.16 Mn ND2 B:Asn467 4.71 Mn O5 B:Ttn603 4.55 Mn O2 B:Ttn603 4.32 Mn C1 B:Ttn603 3.13 Mn O1 B:Ttn603 2.43 Mn C3 B:Ttn603 4.35 Mn O3 B:Ttn603 2.18 Mn C2 B:Ttn603 3.13 Mn O B:Hoh2071 4.51 Mn O B:Hoh2138 2.55 interactive model: Manganese binding site 3 out of 4 in 1gz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1gz4. 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: Arg165, C: Leu167, C: Lys183, C: Glu255, C: Asp256, C: Asp278, C: Asp279, C: Asn467, C: Ttn603, conact list: Atom Atom Distance (A) Mn CZ C:Arg165 4.33 Mn NH2 C:Arg165 3.07 Mn NH1 C:Arg165 4.90 Mn CD2 C:Leu167 4.93 Mn CE C:Lys183 4.59 Mn NZ C:Lys183 3.96 Mn OE1 C:Glu255 2.31 Mn OE2 C:Glu255 4.47 Mn CD C:Glu255 3.35 Mn CG C:Glu255 3.74 Mn N C:Asp256 4.26 Mn CB C:Asp256 4.52 Mn OD2 C:Asp256 3.66 Mn OD1 C:Asp256 2.17 Mn CG C:Asp256 3.24 Mn CA C:Asp256 4.67 Mn OD2 C:Asp278 4.99 Mn CB C:Asp279 4.64 Mn OD2 C:Asp279 3.55 Mn OD1 C:Asp279 2.32 Mn CG C:Asp279 3.28 Mn ND2 C:Asn467 4.84 Mn O5 C:Ttn603 4.28 Mn O2 C:Ttn603 4.20 Mn C1 C:Ttn603 3.04 Mn O1 C:Ttn603 2.21 Mn C3 C:Ttn603 4.28 Mn O3 C:Ttn603 2.36 Mn C2 C:Ttn603 3.22 interactive model: Manganese binding site 4 out of 4 in 1gz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1gz4. 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: Arg165, D: Leu167, D: Lys183, D: Glu255, D: Asp256, D: Asp278, D: Asp279, D: Asn467, D: Ttn603, D: Hoh2087, D: Hoh2146, D: Hoh2147, conact list: Atom Atom Distance (A) Mn CZ D:Arg165 4.39 Mn NH2 D:Arg165 3.24 Mn CD2 D:Leu167 4.99 Mn CE D:Lys183 4.40 Mn NZ D:Lys183 4.39 Mn OE1 D:Glu255 2.32 Mn OE2 D:Glu255 4.45 Mn CD D:Glu255 3.36 Mn CG D:Glu255 3.78 Mn N D:Asp256 4.28 Mn CB D:Asp256 4.58 Mn OD2 D:Asp256 3.73 Mn OD1 D:Asp256 2.33 Mn CG D:Asp256 3.34 Mn CA D:Asp256 4.68 Mn OD2 D:Asp278 4.78 Mn CB D:Asp279 4.50 Mn OD2 D:Asp279 3.32 Mn OD1 D:Asp279 2.22 Mn CG D:Asp279 3.12 Mn ND2 D:Asn467 4.68 Mn O5 D:Ttn603 4.71 Mn O2 D:Ttn603 4.32 Mn C1 D:Ttn603 3.15 Mn O1 D:Ttn603 2.42 Mn C3 D:Ttn603 4.48 Mn O3 D:Ttn603 2.32 Mn C2 D:Ttn603 3.20 Mn O D:Hoh2087 4.47 Mn O D:Hoh2146 4.66 Mn O D:Hoh2147 2.52 interactive model: