Sodium in the structure of Ternary Complex of Dna Polymerase Beta With A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate (pdb 2iso)

The binding sites of Sodium atom in the structure of Ternary Complex of Dna Polymerase Beta With A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate (pdb code 2iso). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2iso structure was solved by C.A.SUCATO, T.G.UPTON, B.A.KASHEMIROV, V.MARTINEK, Y.XIANG, W.A.BEARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.4-2.1 Space group P1211 a (A) 50.700 b (A) 80.500 c (A) 55.400 alpha (°) 90.00 beta (°) 108.00 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 26 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2iso Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2iso. 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: Doc10, A: Asp190, A: Met191, A: Asp192, A: Arg254, A: Asp256, A: Mg339, A: Gff338, P: Hoh377, P: Hoh427, A: Hoh531, conact list: Atom Atom Distance (A) Na OP1 P:Doc10 4.75 Na C3' P:Doc10 3.52 Na C5' P:Doc10 4.52 Na C2' P:Doc10 4.55 Na C4' P:Doc10 4.49 Na O5' P:Doc10 4.64 Na CB A:Asp190 4.25 Na OD2 A:Asp190 2.19 Na OD1 A:Asp190 3.12 Na CG A:Asp190 2.93 Na O A:Met191 4.60 Na CB A:Asp192 4.55 Na OD2 A:Asp192 3.39 Na OD1 A:Asp192 2.22 Na CG A:Asp192 3.16 Na NH2 A:Arg254 4.79 Na CB A:Asp256 4.19 Na OD2 A:Asp256 2.59 Na OD1 A:Asp256 4.68 Na CG A:Asp256 3.67 Na MG A:Mg339 3.33 Na O5' A:Gff338 3.67 Na O2B A:Gff338 4.88 Na O3A A:Gff338 4.87 Na P1 A:Gff338 3.53 Na O2A A:Gff338 4.00 Na C5' A:Gff338 4.04 Na O1G A:Gff338 4.62 Na O1A A:Gff338 2.60 Na O P:Hoh377 4.19 Na O P:Hoh427 2.67 Na O A:Hoh531 4.84 interactive model: Sodium binding site 2 out of 3 in 2iso Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2iso. 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: Dc8, P: Dg9, A: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, P: Hoh27, A: Hoh436, A: Hoh533, A: Hoh534, conact list: Atom Atom Distance (A) Na O3' P:Dc8 4.49 Na OP1 P:Dg9 2.50 Na P P:Dg9 3.49 Na OP2 P:Dg9 3.57 Na O5' P:Dg9 4.70 Na O A:Leu100 4.89 Na O A:Thr101 2.22 Na CB A:Thr101 4.51 Na C A:Thr101 3.26 Na CA A:Thr101 3.94 Na O A:Arg102 4.67 Na N A:Arg102 4.27 Na C A:Arg102 4.23 Na CA A:Arg102 4.53 Na O A:Val103 2.60 Na N A:Val103 4.07 Na C A:Val103 3.49 Na CA A:Val103 4.45 Na N A:Ser104 4.13 Na C A:Ser104 4.41 Na CA A:Ser104 4.07 Na N A:Gly105 4.01 Na C A:Gly105 4.70 Na CA A:Gly105 4.95 Na O A:Ile106 2.48 Na N A:Ile106 3.76 Na CB A:Ile106 4.51 Na C A:Ile106 3.50 Na CA A:Ile106 4.14 Na N A:Gly107 4.51 Na CA A:Gly107 4.76 Na O P:Hoh27 2.48 Na O A:Hoh436 2.72 Na O A:Hoh533 4.73 Na O A:Hoh534 3.82 interactive model: Sodium binding site 3 out of 3 in 2iso Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2iso. 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: D: Dt2, D: Dc3, A: Ala59, A: Lys60, A: Lys61, A: Leu62, A: Pro63, A: Gly64, A: Val65, A: Gly66, D: Hoh364, A: Hoh467, conact list: Atom Atom Distance (A) Na O3' D:Dt2 4.97 Na OP1 D:Dc3 2.80 Na P D:Dc3 3.90 Na OP2 D:Dc3 4.06 Na O5' D:Dc3 4.98 Na O A:Ala59 4.92 Na O A:Lys60 2.22 Na CB A:Lys60 4.70 Na C A:Lys60 3.33 Na CG A:Lys60 4.10 Na CA A:Lys60 4.08 Na NZ A:Lys60 4.80 Na O A:Lys61 4.08 Na N A:Lys61 4.33 Na C A:Lys61 4.02 Na CA A:Lys61 4.52 Na O A:Leu62 2.46 Na N A:Leu62 4.17 Na C A:Leu62 3.45 Na CA A:Leu62 4.44 Na N A:Pro63 4.15 Na C A:Pro63 4.69 Na CA A:Pro63 4.12 Na N A:Gly64 4.36 Na O A:Val65 2.60 Na N A:Val65 4.06 Na CB A:Val65 4.46 Na C A:Val65 3.68 Na CA A:Val65 4.30 Na N A:Gly66 4.73 Na CA A:Gly66 4.98 Na O D:Hoh364 2.52 Na O A:Hoh467 2.63 interactive model: