Sodium in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of MGCL2 (pdb 7ick)

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 MGCL2 (pdb code 7ick). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 7ick 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) 20.0-2.9 Space group P21212 a (A) 178.561 b (A) 57.740 c (A) 48.469 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 7ick Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 7ick. 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 4.72 Na OP1 P:Dg6 2.35 Na P P:Dg6 3.54 Na OP2 P:Dg6 3.86 Na O5' P:Dg6 4.50 Na O A:Leu100 4.89 Na O A:Thr101 2.27 Na CG2 A:Thr101 4.86 Na C A:Thr101 3.36 Na CA A:Thr101 4.20 Na O A:Arg102 4.24 Na N A:Arg102 4.26 Na C A:Arg102 3.90 Na CA A:Arg102 4.32 Na O A:Val103 2.41 Na N A:Val103 3.81 Na C A:Val103 3.19 Na CA A:Val103 4.12 Na N A:Ser104 3.86 Na C A:Ser104 4.29 Na CA A:Ser104 3.93 Na N A:Gly105 3.93 Na C A:Gly105 4.72 Na CA A:Gly105 4.95 Na O A:Ile106 2.49 Na N A:Ile106 3.78 Na CB A:Ile106 4.65 Na C A:Ile106 3.57 Na CA A:Ile106 4.20 Na N A:Gly107 4.62 Na CA A:Gly107 4.92 Na O A:Hoh601 3.30 interactive model: Sodium binding site 2 out of 2 in 7ick Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 7ick. 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 3.50 Na P P:Dg3 4.24 Na OP2 P:Dg3 4.04 Na O P:Hoh615 4.50 interactive model: