Rubidium in the structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna (pdb 3ggk)

The binding sites of Rubidium atom in the structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna (pdb code 3ggk). This binding sites where shown with 5.0 Angstroms radius around Rubidium atom. The 3ggk structure was solved by T.MAEHIGASHI, T.MOULAEI, D.WATKINS, S.KOMEDA, L.D.WILLIAMS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.6-0.9 Space group C121 a (A) 32.135 b (A) 25.156 c (A) 34.113 alpha (°) 90.00 beta (°) 116.24 gamma (°) 90.00 Rfactor (%) 11.9 Rfree (%) 13.4 Rubidium Binding Sites: Rubidium binding site 1 out of 2 in 3ggk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Rubidium in the PDB 3ggk. 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: Dg10, A: Mg22, A: Rb102, A: Hoh238, A: Hoh260, A: Hoh282, A: Hoh299, A: Hoh300, A: Hoh301, A: Hoh302, A: Hoh303, conact list: Atom Atom Distance (A) Rb N7 A:Dg9 4.94 Rb C6 A:Dg10 3.85 Rb C5 A:Dg10 4.31 Rb N7 A:Dg10 4.09 Rb O6 A:Dg10 2.92 Rb MG A:Mg22 4.64 Rb MG A:Mg22 4.02 Rb RB A:Rb102 2.75 Rb O A:Hoh238 4.81 Rb O A:Hoh238 4.89 Rb O A:Hoh260 3.06 Rb O A:Hoh282 3.10 Rb O A:Hoh299 3.51 Rb O A:Hoh299 3.59 Rb O A:Hoh300 4.82 Rb O A:Hoh301 2.35 Rb O A:Hoh302 3.51 Rb O A:Hoh302 4.83 Rb O A:Hoh303 4.31 interactive model: Rubidium binding site 2 out of 2 in 3ggk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Rubidium in the PDB 3ggk. 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: Dt8, A: Dg9, A: Dg10, A: Mg22, A: Rb101, A: Hoh205, A: Hoh219, A: Hoh238, A: Hoh260, A: Hoh269, A: Hoh270, A: Hoh282, A: Hoh298, A: Hoh299, A: Hoh300, A: Hoh301, A: Hoh302, A: Hoh303, conact list: Atom Atom Distance (A) Rb C2' A:Dt8 4.87 Rb N9 A:Dg9 4.99 Rb C8 A:Dg9 3.85 Rb C6 A:Dg9 4.29 Rb C5 A:Dg9 3.90 Rb N7 A:Dg9 2.98 Rb O6 A:Dg9 3.97 Rb C6 A:Dg10 4.09 Rb C5 A:Dg10 4.65 Rb N7 A:Dg10 4.50 Rb O6 A:Dg10 3.07 Rb MG A:Mg22 2.43 Rb MG A:Mg22 4.51 Rb RB A:Rb101 2.75 Rb O A:Hoh205 4.84 Rb O A:Hoh219 4.97 Rb O A:Hoh238 3.13 Rb O A:Hoh238 2.65 Rb O A:Hoh260 4.34 Rb O A:Hoh269 2.77 Rb O A:Hoh270 3.65 Rb O A:Hoh282 3.43 Rb O A:Hoh298 3.81 Rb O A:Hoh299 2.69 Rb O A:Hoh299 3.19 Rb O A:Hoh300 3.33 Rb O A:Hoh301 3.13 Rb O A:Hoh301 3.74 Rb O A:Hoh302 0.85 Rb O A:Hoh302 4.32 Rb O A:Hoh303 4.52 interactive model: