Sodium in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Seven Base Pairs Of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb 8icv)

The binding sites of Sodium atom in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Seven Base Pairs Of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8icv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 8icv 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) 179.019 b (A) 57.629 c (A) 48.283 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.9 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 8icv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 8icv. 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: Da5, P: Dt6, 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:Da5 4.11 Na OP1 P:Dt6 1.80 Na P P:Dt6 3.12 Na OP2 P:Dt6 3.69 Na O5' P:Dt6 4.20 Na O A:Thr101 2.16 Na CG2 A:Thr101 4.97 Na C A:Thr101 3.40 Na CA A:Thr101 4.38 Na O A:Arg102 4.47 Na N A:Arg102 4.31 Na C A:Arg102 4.06 Na CA A:Arg102 4.39 Na O A:Val103 2.53 Na N A:Val103 3.98 Na C A:Val103 3.51 Na CA A:Val103 4.39 Na N A:Ser104 4.23 Na C A:Ser104 4.34 Na CA A:Ser104 4.03 Na N A:Gly105 3.67 Na C A:Gly105 4.43 Na CA A:Gly105 4.67 Na O A:Ile106 2.51 Na N A:Ile106 3.71 Na CB A:Ile106 4.30 Na CG2 A:Ile106 4.77 Na C A:Ile106 3.52 Na CA A:Ile106 4.05 Na N A:Gly107 4.59 Na CA A:Gly107 4.92 Na O A:Hoh601 2.06 interactive model: Sodium binding site 2 out of 2 in 8icv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 8icv. 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, conact list: Atom Atom Distance (A) Na O A:Lys60 2.98 Na CE A:Lys60 4.78 Na C A:Lys60 4.19 Na CG A:Lys60 4.63 Na O A:Lys61 4.20 Na N A:Lys61 4.93 Na C A:Lys61 4.22 Na CA A:Lys61 4.74 Na O A:Leu62 2.67 Na N A:Leu62 4.42 Na C A:Leu62 3.70 Na CA A:Leu62 4.63 Na N A:Pro63 4.53 Na CA A:Pro63 4.62 Na N A:Gly64 4.95 Na O A:Val65 3.13 Na N A:Val65 4.59 Na C A:Val65 4.20 Na CA A:Val65 4.73 interactive model: