Sodium in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 (pdb 7icn)

The binding sites of Sodium atom in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 (pdb code 7icn). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 7icn 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) 20.0-2.8 Space group P21212 a (A) 178.573 b (A) 57.754 c (A) 48.512 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.2 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 7icn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 7icn. 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 4.48 Na OP1 P:Dg6 2.73 Na P P:Dg6 3.51 Na OP2 P:Dg6 3.35 Na O5' P:Dg6 4.83 Na O A:Leu100 4.83 Na O A:Thr101 2.12 Na CB A:Thr101 4.85 Na CG2 A:Thr101 4.42 Na C A:Thr101 3.30 Na CA A:Thr101 4.10 Na O A:Arg102 4.31 Na N A:Arg102 4.30 Na C A:Arg102 4.00 Na CA A:Arg102 4.50 Na O A:Val103 2.40 Na N A:Val103 3.82 Na CB A:Val103 4.94 Na C A:Val103 3.16 Na CA A:Val103 4.03 Na N A:Ser104 3.85 Na C A:Ser104 4.31 Na CA A:Ser104 3.97 Na N A:Gly105 4.05 Na C A:Gly105 4.57 Na CA A:Gly105 4.96 Na O A:Ile106 2.50 Na N A:Ile106 3.54 Na CB A:Ile106 4.12 Na C A:Ile106 3.36 Na CA A:Ile106 3.79 Na N A:Gly107 4.38 Na CA A:Gly107 4.66 Na O A:Hoh601 3.28 interactive model: Sodium binding site 2 out of 2 in 7icn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 7icn. 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 3.63 Na P P:Dg3 4.20 Na OP2 P:Dg3 3.76 Na O P:Hoh615 4.41 interactive model: