Sodium in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs Of Dna; Soaked in the Presence of CUCL2 (0.1 Millimolar) (pdb 7icj)

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; Soaked in the Presence of CUCL2 (0.1 Millimolar) (pdb code 7icj). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 7icj 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) 20.0-3.5 Space group P21212 a (A) 177.010 b (A) 57.749 c (A) 48.582 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.3 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 1 in 7icj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 7icj. 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: A: Ala59, A: Lys60, A: Leu62, A: Pro63, A: Gly64, A: Val65, A: Gly66, conact list: Atom Atom Distance (A) Na O A:Ala59 4.99 Na O A:Lys60 3.91 Na C A:Lys60 4.74 Na O A:Leu62 2.15 Na N A:Leu62 4.62 Na CB A:Leu62 4.66 Na C A:Leu62 3.00 Na CA A:Leu62 4.25 Na O A:Pro63 3.93 Na N A:Pro63 3.49 Na CB A:Pro63 4.80 Na CD A:Pro63 4.97 Na C A:Pro63 3.04 Na CA A:Pro63 3.29 Na O A:Gly64 3.50 Na N A:Gly64 2.48 Na C A:Gly64 2.69 Na CA A:Gly64 3.14 Na O A:Val65 2.60 Na N A:Val65 2.11 Na CB A:Val65 3.50 Na CG2 A:Val65 4.12 Na C A:Val65 2.76 Na CG1 A:Val65 4.82 Na CA A:Val65 2.76 Na N A:Gly66 3.75 Na CA A:Gly66 4.60 interactive model: