The binding sites of Rubidium atom in the structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove (pdb code 461d). This binding sites where shown with 5.0 Angstroms radius around Rubidium atom. The 461d structure was solved by V.TERESHKO, G.MINASOV, M.EGLI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 20.0-1.5 | Space group | P212121 | a (A) | 25.070 | b (A) | 39.720 | c (A) | 65.770 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 18.6 | Rfree (%) | n/a |
|
Rubidium binding site 1 out of 1 in 461d
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Rubidium in the PDB 461d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Rubidium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Da6, A: Taf7, A: Dt8, B: Da18, B: Taf19, B: Dt20, A: Hoh104, A: Hoh131, A: Hoh265, B: Hoh115, B: Hoh145, | conact list:
Atom | Atom | Distance (A) | Rb | C2 A:Da6 | 4.57 | Rb | N3 A:Taf7 | 4.97 | Rb | C2 A:Taf7 | 3.98 | Rb | N1 A:Taf7 | 4.70 | Rb | C1' A:Taf7 | 4.34 | Rb | O2 A:Taf7 | 2.82 | Rb | C2 A:Dt8 | 4.99 | Rb | N1 A:Dt8 | 4.83 | Rb | C1' A:Dt8 | 4.41 | Rb | O2 A:Dt8 | 4.83 | Rb | O4' A:Dt8 | 3.47 | Rb | C5' A:Dt8 | 4.38 | Rb | C4' A:Dt8 | 3.96 | Rb | C2 B:Da18 | 4.45 | Rb | N3 B:Taf19 | 4.89 | Rb | C2 B:Taf19 | 3.89 | Rb | N1 B:Taf19 | 4.61 | Rb | C1' B:Taf19 | 4.26 | Rb | O2 B:Taf19 | 2.71 | Rb | C2 B:Dt20 | 5.00 | Rb | N1 B:Dt20 | 4.74 | Rb | C1' B:Dt20 | 4.30 | Rb | O2 B:Dt20 | 4.92 | Rb | O4' B:Dt20 | 3.30 | Rb | C5' B:Dt20 | 4.09 | Rb | C4' B:Dt20 | 3.75 | Rb | O A:Hoh104 | 4.72 | Rb | O A:Hoh131 | 2.80 | Rb | O A:Hoh265 | 3.21 | Rb | O B:Hoh115 | 4.89 | Rb | O B:Hoh145 | 2.77 |
| interactive model:
|
|