Rubidium in the structure of 1.05 A Structure Of the A-Decamer Gcgtatacgc With A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt (pdb 1i0m)

The binding sites of Rubidium atom in the structure of 1.05 A Structure Of the A-Decamer Gcgtatacgc With A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt (pdb code 1i0m). This binding sites where shown with 5.0 Angstroms radius around Rubidium atom. The 1i0m structure was solved by V.TERESHKO, C.J.WILDS, G.MINASOV, T.P.PRAKASH, M.A.MAIER, A.HOWARD, Z.WAWRZAK, M.MANOHARAN, M.EGLI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.1 Space group P212121 a (A) 24.820 b (A) 45.260 c (A) 43.970 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.4 Rfree (%) 17 Rubidium Binding Sites: Rubidium binding site 1 out of 3 in 1i0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Rubidium in the PDB 1i0m. 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: Dg9, A: Dc10, A: Hoh175, A: Hoh244, conact list: Atom Atom Distance (A) Rb C3' A:Dg9 4.24 Rb O3' A:Dg9 3.04 Rb C2' A:Dg9 4.92 Rb C4' A:Dg9 4.49 Rb OP1 A:Dc10 2.99 Rb P A:Dc10 3.66 Rb OP2 A:Dc10 4.83 Rb C5' A:Dc10 4.48 Rb O5' A:Dc10 4.59 Rb O A:Hoh175 4.89 Rb O A:Hoh244 4.67 interactive model: Rubidium binding site 2 out of 3 in 1i0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Rubidium in the PDB 1i0m. 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: Dg3, A: Dt4, A: Da5, B: 12516, B: Da17, A: Hoh135, A: Hoh136, A: Hoh164, A: Hoh194, A: Hoh208, A: Hoh305, A: Hoh311, A: Hoh347, B: Hoh219, B: Hoh282, B: Hoh308, B: Hoh341, conact list: Atom Atom Distance (A) Rb C8 A:Dg3 4.35 Rb C6 A:Dg3 3.61 Rb N1 A:Dg3 4.71 Rb C5 A:Dg3 3.65 Rb N7 A:Dg3 3.38 Rb C4 A:Dg3 4.74 Rb O6 A:Dg3 3.27 Rb C5 A:Dt4 4.43 Rb C7 A:Dt4 3.80 Rb C4 A:Dt4 4.00 Rb O4 A:Dt4 2.98 Rb N6 A:Da5 4.03 Rb O4 B:12516 4.94 Rb N6 B:Da17 4.25 Rb O A:Hoh135 4.87 Rb O A:Hoh136 2.98 Rb O A:Hoh164 3.57 Rb O A:Hoh194 4.76 Rb O A:Hoh208 3.26 Rb O A:Hoh305 3.89 Rb O A:Hoh311 4.98 Rb O A:Hoh347 3.98 Rb O B:Hoh219 3.67 Rb O B:Hoh282 3.73 Rb O B:Hoh308 3.29 Rb O B:Hoh341 4.95 interactive model: Rubidium binding site 3 out of 3 in 1i0m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Rubidium in the PDB 1i0m. 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: Dg9, A: Dc10, A: Hoh159, A: Hoh165, A: Hoh175, A: Hoh185, A: Hoh195, A: Hoh302, A: Hoh317, A: Hoh338, conact list: Atom Atom Distance (A) Rb OP1 A:Dg9 4.99 Rb O3' A:Dg9 4.81 Rb OP1 A:Dc10 3.94 Rb P A:Dc10 3.85 Rb OP2 A:Dc10 2.84 Rb O A:Hoh159 4.13 Rb O A:Hoh165 4.67 Rb O A:Hoh175 2.50 Rb O A:Hoh185 1.71 Rb O A:Hoh195 2.71 Rb O A:Hoh302 4.15 Rb O A:Hoh317 4.08 Rb O A:Hoh338 4.78 interactive model: