Sodium in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs of Dna; Native Structure (pdb 9icw)

The binding sites of Sodium atom in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs of Dna; Native Structure (pdb code 9icw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 9icw structure was solved by H.PELLETIER, M.R.SAWAYA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.6 Space group P21212 a (A) 178.638 b (A) 57.846 c (A) 48.489 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 9icw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 9icw. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: Dt5, P: Dg6, A: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, A: Hoh601, conact list: Atom Atom Distance (A) Na O3' P:Dt5 4.61 Na OP1 P:Dg6 2.48 Na P P:Dg6 3.51 Na OP2 P:Dg6 3.63 Na O5' P:Dg6 4.72 Na O A:Leu100 4.87 Na O A:Thr101 2.27 Na CB A:Thr101 4.97 Na CG2 A:Thr101 4.72 Na C A:Thr101 3.38 Na CA A:Thr101 4.13 Na O A:Arg102 4.59 Na N A:Arg102 4.37 Na C A:Arg102 4.19 Na CA A:Arg102 4.52 Na O A:Val103 2.39 Na N A:Val103 4.08 Na C A:Val103 3.43 Na CA A:Val103 4.43 Na N A:Ser104 4.13 Na C A:Ser104 4.36 Na CA A:Ser104 3.98 Na N A:Gly105 3.95 Na C A:Gly105 4.69 Na CA A:Gly105 4.91 Na O A:Ile106 2.34 Na N A:Ile106 3.76 Na CB A:Ile106 4.44 Na C A:Ile106 3.44 Na CA A:Ile106 4.11 Na N A:Gly107 4.44 Na CA A:Gly107 4.69 Na O A:Hoh601 3.30 interactive model: Sodium binding site 2 out of 2 in 9icw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 9icw. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: Dg3, P: Hoh615, conact list: Atom Atom Distance (A) Na OP1 P:Dg3 3.47 Na P P:Dg3 4.03 Na OP2 P:Dg3 3.61 Na O P:Hoh615 4.54 interactive model: