The binding sites of Manganese atom in the structure of Hiv-1 Dis Rna Subtype F- Mn Soaked (pdb code 1y3o). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1y3o structure was solved by E.ENNIFAR, P.DUMAS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 10.0-2.7 | Space group | C2221 | a (A) | 27.341 | b (A) | 117.358 | c (A) | 94.672 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 22 | Rfree (%) | 28 |
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Manganese binding site 1 out of 4 in 1y3o
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1y3o. 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: G10, B: A16, | conact list:
Atom | Atom | Distance (A) | Mn | N9 A:G10 | 4.71 | Mn | OP1 A:G10 | 4.53 | Mn | C8 A:G10 | 3.46 | Mn | C6 A:G10 | 4.12 | Mn | C5 A:G10 | 3.65 | Mn | N7 A:G10 | 2.57 | Mn | C4 A:G10 | 4.81 | Mn | O6 A:G10 | 3.82 | Mn | C2 B:A16 | 4.85 | Mn | N1 B:A16 | 4.26 |
| interactive model:
| Manganese binding site 2 out of 4 in 1y3o
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1y3o. 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: A16, B: G10, | conact list:
Atom | Atom | Distance (A) | Mn | N1 A:A16 | 4.54 | Mn | N9 B:G10 | 4.62 | Mn | OP1 B:G10 | 4.42 | Mn | C8 B:G10 | 3.40 | Mn | C6 B:G10 | 3.88 | Mn | C5 B:G10 | 3.47 | Mn | N7 B:G10 | 2.44 | Mn | C4 B:G10 | 4.66 | Mn | O6 B:G10 | 3.56 |
| interactive model:
| Manganese binding site 3 out of 4 in 1y3o
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1y3o. 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: U6, A: G7, | conact list:
Atom | Atom | Distance (A) | Mn | C5 A:U6 | 4.96 | Mn | C4 A:U6 | 4.94 | Mn | O4 A:U6 | 4.42 | Mn | C6 A:G7 | 4.89 | Mn | N7 A:G7 | 4.43 | Mn | O6 A:G7 | 4.05 |
| interactive model:
| Manganese binding site 4 out of 4 in 1y3o
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1y3o. 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: U11, A: G12, A: C13, B: U11, B: G12, B: C13, | conact list:
Atom | Atom | Distance (A) | Mn | O4 A:U11 | 4.38 | Mn | C6 A:G12 | 4.98 | Mn | O6 A:G12 | 3.85 | Mn | N4 A:C13 | 4.60 | Mn | O4 B:U11 | 4.79 | Mn | C6 B:G12 | 4.95 | Mn | O6 B:G12 | 3.85 | Mn | N4 B:C13 | 4.62 |
| interactive model:
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