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 |
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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:
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