Sodium in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2 (pdb 9icb)

The binding sites of Sodium atom in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2 (pdb code 9icb). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 9icb 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) 20.0-3.2 Space group P21212 a (A) 178.884 b (A) 57.712 c (A) 48.421 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.2 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 9icb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 9icb. 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: Dt6, A: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, P: Hoh601, conact list: Atom Atom Distance (A) Na OP1 P:Dt6 2.78 Na P P:Dt6 3.84 Na OP2 P:Dt6 3.98 Na O5' P:Dt6 4.65 Na O A:Leu100 4.94 Na O A:Thr101 2.07 Na C A:Thr101 3.16 Na CA A:Thr101 4.37 Na O A:Arg102 3.21 Na N A:Arg102 3.76 Na CB A:Arg102 4.97 Na C A:Arg102 3.10 Na CA A:Arg102 3.54 Na O A:Val103 2.67 Na N A:Val103 3.41 Na C A:Val103 3.11 Na CA A:Val103 3.84 Na N A:Ser104 3.68 Na C A:Ser104 4.56 Na CA A:Ser104 3.91 Na N A:Gly105 4.37 Na O A:Ile106 2.91 Na N A:Ile106 4.13 Na CB A:Ile106 4.68 Na C A:Ile106 4.00 Na CA A:Ile106 4.50 Na O P:Hoh601 2.17 interactive model: Sodium binding site 2 out of 2 in 9icb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 9icb. 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: Lys60, A: Lys61, A: Leu62, A: Pro63, A: Gly64, A: Val65, A: Hoh656, conact list: Atom Atom Distance (A) Na O A:Lys60 3.00 Na C A:Lys60 4.13 Na O A:Lys61 3.93 Na N A:Lys61 4.88 Na C A:Lys61 4.02 Na CA A:Lys61 4.75 Na O A:Leu62 1.97 Na N A:Leu62 4.13 Na C A:Leu62 3.06 Na CA A:Leu62 4.14 Na N A:Pro63 3.86 Na CD A:Pro63 4.64 Na C A:Pro63 4.65 Na CA A:Pro63 3.99 Na N A:Gly64 4.32 Na O A:Val65 3.28 Na N A:Val65 4.27 Na CG2 A:Val65 4.55 Na C A:Val65 4.24 Na CA A:Val65 4.69 Na O A:Hoh656 3.27 interactive model: