Sodium in the structure of Ternary Complex Structure Of Dna Polymerase Beta With A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer (pdb 3tfs)

The binding sites of Sodium atom in the structure of Ternary Complex Structure Of Dna Polymerase Beta With A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer (pdb code 3tfs). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3tfs structure was solved by B.T.CHAMBERLAIN, V.K.BATRA, W.A.BEARD, A.P.KADINA, D.D.SHOCK, B.A.KASHEMIROV, C.E.MCKENNA, M.F.GOODMAN, S.H.WILSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.6-2.0 Space group P1211 a (A) 50.770 b (A) 79.580 c (A) 55.720 alpha (°) 90.00 beta (°) 107.75 gamma (°) 90.00 Rfactor (%) 18.8 Rfree (%) 24.2 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3tfs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3tfs. 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: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, P: Dc8, P: Dg9, A: Hoh485, A: Hoh513, P: Hoh78, conact list: Atom Atom Distance (A) Na O A:Leu100 4.91 Na O A:Thr101 2.48 Na CB A:Thr101 4.51 Na C A:Thr101 3.40 Na CA A:Thr101 3.98 Na O A:Arg102 4.67 Na N A:Arg102 4.40 Na C A:Arg102 4.28 Na CA A:Arg102 4.61 Na O A:Val103 2.67 Na N A:Val103 4.12 Na C A:Val103 3.45 Na CA A:Val103 4.43 Na N A:Ser104 4.02 Na C A:Ser104 4.28 Na CA A:Ser104 3.92 Na N A:Gly105 4.03 Na C A:Gly105 4.72 Na CA A:Gly105 4.91 Na O A:Ile106 2.60 Na N A:Ile106 3.90 Na CB A:Ile106 4.66 Na C A:Ile106 3.59 Na CA A:Ile106 4.27 Na N A:Gly107 4.52 Na CA A:Gly107 4.71 Na O3' P:Dc8 4.46 Na OP1 P:Dg9 2.53 Na P P:Dg9 3.47 Na OP2 P:Dg9 3.50 Na O5' P:Dg9 4.66 Na O A:Hoh485 3.79 Na O A:Hoh513 2.65 Na O P:Hoh78 2.69 interactive model: Sodium binding site 2 out of 2 in 3tfs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3tfs. 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: Gly66, D: Dt2, D: Dc3, A: Hoh506, A: Hoh617, conact list: Atom Atom Distance (A) Na O A:Lys60 2.64 Na C A:Lys60 3.66 Na CG A:Lys60 4.50 Na CA A:Lys60 4.38 Na O A:Lys61 4.15 Na N A:Lys61 4.59 Na C A:Lys61 4.08 Na CA A:Lys61 4.68 Na O A:Leu62 2.57 Na N A:Leu62 4.10 Na C A:Leu62 3.41 Na CA A:Leu62 4.37 Na N A:Pro63 4.06 Na C A:Pro63 4.41 Na CA A:Pro63 4.03 Na N A:Gly64 4.07 Na C A:Gly64 4.81 Na O A:Val65 2.58 Na N A:Val65 3.86 Na CB A:Val65 4.49 Na C A:Val65 3.65 Na CA A:Val65 4.20 Na N A:Gly66 4.75 Na O3' D:Dt2 4.58 Na OP1 D:Dc3 2.70 Na P D:Dc3 3.61 Na OP2 D:Dc3 3.68 Na O5' D:Dc3 4.87 Na O A:Hoh506 2.89 Na O A:Hoh617 2.72 interactive model: