Potassium in the structure of Crystal Structure of Manganese Bound M-Box Rna (pdb 3pdr)
The binding sites of Potassium atom in the structure of Crystal Structure of Manganese Bound M-Box Rna (pdb code 3pdr). This binding sites where shown with 5.0 Angstroms radius around Potassium atom. The 3pdr structure was solved by A RAMESH, W.C.WINKLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 47.5-1.9 | Space group | P212121 | a (A) | 68.780 | b (A) | 102.487 | c (A) | 126.375 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 19.2 | Rfree (%) | 22.8 |
|
Potassium Binding Sites:Potassium binding site 1 out of 6 in 3pdr
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G27, X: U28, X: G29, X: A155, X: A156, X: G157, X: C158, X: Hoh212, X: Hoh213, X: Hoh236, X: Hoh266, X: Hoh342, | conact list:
Atom | Atom | Distance (A) | K | C6 X:G27 | 4.43 | K | O6 X:G27 | 3.39 | K | N3 X:U28 | 3.94 | K | C4 X:U28 | 3.86 | K | O4 X:U28 | 2.97 | K | N3 X:G29 | 4.95 | K | N2 X:G29 | 3.81 | K | C2 X:G29 | 4.05 | K | C6 X:G29 | 4.72 | K | N1 X:G29 | 3.87 | K | OP1 X:A155 | 4.65 | K | P X:A155 | 3.97 | K | OP2 X:A155 | 2.93 | K | C5' X:A155 | 3.70 | K | O5' X:A155 | 4.18 | K | OP1 X:A156 | 4.71 | K | C6 X:G157 | 4.02 | K | C5 X:G157 | 4.57 | K | N7 X:G157 | 4.39 | K | O6 X:G157 | 3.00 | K | N3 X:C158 | 4.88 | K | C4 X:C158 | 4.34 | K | N4 X:C158 | 3.31 | K | O X:Hoh212 | 3.02 | K | O X:Hoh213 | 4.67 | K | O X:Hoh236 | 4.40 | K | O X:Hoh266 | 3.60 | K | O X:Hoh342 | 3.07 |
| interactive model:
| Potassium binding site 2 out of 6 in 3pdr
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G66, X: U67, X: C68, X: A74, X: C75, X: A106, X: G107, X: Hoh186, | conact list:
Atom | Atom | Distance (A) | K | N2 X:G66 | 4.01 | K | C2 X:G66 | 4.93 | K | C2 X:U67 | 4.10 | K | N1 X:U67 | 4.76 | K | C1' X:U67 | 4.31 | K | O2 X:U67 | 2.95 | K | C2' X:U67 | 4.45 | K | O2' X:U67 | 4.06 | K | O4' X:C68 | 4.67 | K | N3 X:A74 | 4.91 | K | C2 X:A74 | 4.29 | K | C2 X:C75 | 4.20 | K | N1 X:C75 | 4.88 | K | C1' X:C75 | 4.63 | K | O2 X:C75 | 3.21 | K | C3' X:A106 | 4.01 | K | O3' X:A106 | 3.18 | K | C2' X:A106 | 4.27 | K | C4' X:A106 | 4.10 | K | O2' X:A106 | 3.35 | K | OP1 X:G107 | 3.97 | K | P X:G107 | 4.25 | K | O5' X:G107 | 4.90 | K | O X:Hoh186 | 3.27 |
| interactive model:
| Potassium binding site 3 out of 6 in 3pdr
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: A25, X: A72, X: G73, X: A162, X: Hoh538, | conact list:
Atom | Atom | Distance (A) | K | N9 X:A25 | 4.81 | K | C1' X:A25 | 4.07 | K | O4' X:A25 | 4.10 | K | O3' X:A72 | 4.32 | K | OP1 X:G73 | 3.48 | K | P X:G73 | 4.61 | K | C1' X:A162 | 4.86 | K | O2' X:A162 | 4.78 | K | O X:Hoh538 | 3.62 |
| interactive model:
| Potassium binding site 4 out of 6 in 3pdr
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G27, A: U28, A: G29, A: A155, A: A156, A: G157, A: C158, A: Hoh181, A: Hoh225, A: Hoh235, A: Hoh260, A: Hoh276, | conact list:
Atom | Atom | Distance (A) | K | C6 A:G27 | 4.52 | K | O6 A:G27 | 3.52 | K | N3 A:U28 | 3.84 | K | C4 A:U28 | 3.81 | K | O4 A:U28 | 2.95 | K | N3 A:G29 | 4.77 | K | N2 A:G29 | 3.63 | K | C2 A:G29 | 3.87 | K | C6 A:G29 | 4.59 | K | N1 A:G29 | 3.73 | K | O6 A:G29 | 4.98 | K | OP1 A:A155 | 4.54 | K | P A:A155 | 3.94 | K | OP2 A:A155 | 2.89 | K | C5' A:A155 | 3.85 | K | O5' A:A155 | 4.30 | K | OP1 A:A156 | 4.90 | K | C6 A:G157 | 3.88 | K | C5 A:G157 | 4.44 | K | N7 A:G157 | 4.28 | K | O6 A:G157 | 2.87 | K | N3 A:C158 | 4.82 | K | C4 A:C158 | 4.19 | K | N4 A:C158 | 3.18 | K | O A:Hoh181 | 2.97 | K | O A:Hoh225 | 3.08 | K | O A:Hoh235 | 4.66 | K | O A:Hoh260 | 3.52 | K | O A:Hoh276 | 4.43 |
| interactive model:
| Potassium binding site 5 out of 6 in 3pdr
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G66, A: U67, A: C68, A: A74, A: C75, A: A106, A: G107, A: Hoh228, A: Hoh270, A: Hoh349, | conact list:
Atom | Atom | Distance (A) | K | N2 A:G66 | 3.82 | K | C2 A:G66 | 4.85 | K | N3 A:U67 | 4.92 | K | C2 A:U67 | 4.03 | K | N1 A:U67 | 4.82 | K | C1' A:U67 | 4.53 | K | O2 A:U67 | 2.90 | K | C2' A:U67 | 4.72 | K | O2' A:U67 | 4.44 | K | O4' A:C68 | 4.76 | K | N3 A:A74 | 4.59 | K | C2 A:A74 | 4.11 | K | N1 A:A74 | 4.95 | K | N3 A:C75 | 4.93 | K | C2 A:C75 | 4.07 | K | N1 A:C75 | 4.71 | K | C1' A:C75 | 4.40 | K | O2 A:C75 | 3.07 | K | O2' A:C75 | 4.75 | K | C3' A:A106 | 4.00 | K | O3' A:A106 | 3.16 | K | C2' A:A106 | 4.15 | K | C4' A:A106 | 4.16 | K | O2' A:A106 | 3.14 | K | OP1 A:G107 | 3.93 | K | P A:G107 | 4.20 | K | O5' A:G107 | 4.72 | K | O A:Hoh228 | 4.35 | K | O A:Hoh270 | 3.21 | K | O A:Hoh349 | 3.40 |
| interactive model:
| Potassium binding site 6 out of 6 in 3pdr
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A25, A: A72, A: G73, A: A162, A: Hoh353, A: Hoh530, | conact list:
Atom | Atom | Distance (A) | K | C1' A:A25 | 4.64 | K | O4' A:A25 | 4.86 | K | O3' A:A72 | 4.73 | K | OP1 A:G73 | 3.99 | K | C1' A:A162 | 4.80 | K | O2' A:A162 | 4.58 | K | O A:Hoh353 | 3.76 | K | O A:Hoh530 | 3.64 |
| interactive model:
|
|
|
|
|