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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb 8ics)

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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8ics). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 8ics 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) 178.792 b (A) 57.623 c (A) 48.419 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.7 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 8ics Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 8ics. 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: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, P: Hoh601, conact list: Atom Atom Distance (A) Na O3' P:Da5 4.95 Na OP1 P:Dt6 2.48 Na P P:Dt6 3.68 Na OP2 P:Dt6 4.05 Na O5' P:Dt6 4.48 Na O A:Leu100 4.78 Na O A:Thr101 2.16 Na C A:Thr101 3.30 Na CA A:Thr101 4.25 Na O A:Arg102 3.90 Na N A:Arg102 4.15 Na C A:Arg102 3.63 Na CA A:Arg102 4.15 Na O A:Val103 2.18 Na N A:Val103 3.59 Na CB A:Val103 4.82 Na C A:Val103 2.96 Na CA A:Val103 3.85 Na N A:Ser104 3.67 Na C A:Ser104 4.31 Na CA A:Ser104 3.76 Na N A:Gly105 4.04 Na C A:Gly105 4.74 Na O A:Ile106 2.53 Na N A:Ile106 3.75 Na CB A:Ile106 4.49 Na C A:Ile106 3.62 Na CA A:Ile106 4.13 Na N A:Gly107 4.73 Na O P:Hoh601 2.35 interactive model: Sodium binding site 2 out of 2 in 8ics Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 8ics. 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 3.41 Na C A:Lys60 4.60 Na O A:Lys61 4.26 Na C A:Lys61 4.33 Na CA A:Lys61 4.95 Na O A:Leu62 2.36 Na N A:Leu62 4.48 Na C A:Leu62 3.39 Na CA A:Leu62 4.52 Na N A:Pro63 4.04 Na CD A:Pro63 4.76 Na C A:Pro63 4.81 Na CA A:Pro63 4.03 Na N A:Gly64 4.63 Na O A:Val65 4.07 Na N A:Val65 4.79 Na C A:Val65 4.90 interactive model: