Sodium in the structure of Ternary Complex Structure of Dna Polymerase Beta With A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site (pdb 3tfr)

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(CF2)Pp in the Active Site (pdb code 3tfr). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3tfr 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) 20.7-2.0 Space group P1211 a (A) 50.890 b (A) 79.380 c (A) 55.650 alpha (°) 90.00 beta (°) 107.64 gamma (°) 90.00 Rfactor (%) 18.8 Rfree (%) 25.1 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3tfr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3tfr. 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: Hoh539, A: Hoh561, A: Hoh653, P: Hoh94, conact list: Atom Atom Distance (A) Na O A:Leu100 4.87 Na O A:Thr101 2.56 Na CB A:Thr101 4.34 Na C A:Thr101 3.36 Na CA A:Thr101 3.86 Na O A:Arg102 4.70 Na N A:Arg102 4.34 Na C A:Arg102 4.26 Na CA A:Arg102 4.59 Na O A:Val103 2.56 Na N A:Val103 4.06 Na C A:Val103 3.42 Na CA A:Val103 4.38 Na N A:Ser104 4.06 Na C A:Ser104 4.33 Na CA A:Ser104 3.99 Na N A:Gly105 4.00 Na C A:Gly105 4.66 Na CA A:Gly105 4.91 Na O A:Ile106 2.57 Na N A:Ile106 3.74 Na CB A:Ile106 4.48 Na C A:Ile106 3.50 Na CA A:Ile106 4.10 Na N A:Gly107 4.49 Na CA A:Gly107 4.75 Na O3' P:Dc8 4.44 Na OP1 P:Dg9 2.54 Na P P:Dg9 3.43 Na OP2 P:Dg9 3.48 Na O5' P:Dg9 4.66 Na O A:Hoh539 3.70 Na O A:Hoh561 2.72 Na O A:Hoh653 4.79 Na O P:Hoh94 2.78 interactive model: Sodium binding site 2 out of 2 in 3tfr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3tfr. 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: Ala59, A: Lys60, A: Lys61, A: Leu62, A: Pro63, A: Gly64, A: Val65, A: Gly66, D: Dt2, D: Dc3, A: Hoh476, A: Hoh725, D: Hoh164, conact list: Atom Atom Distance (A) Na O A:Ala59 4.95 Na O A:Lys60 2.59 Na CB A:Lys60 4.99 Na C A:Lys60 3.61 Na CG A:Lys60 4.37 Na CA A:Lys60 4.33 Na NZ A:Lys60 4.95 Na O A:Lys61 4.29 Na N A:Lys61 4.55 Na C A:Lys61 4.10 Na CA A:Lys61 4.66 Na O A:Leu62 2.67 Na N A:Leu62 4.04 Na C A:Leu62 3.41 Na CA A:Leu62 4.34 Na N A:Pro63 4.02 Na C A:Pro63 4.46 Na CA A:Pro63 4.03 Na N A:Gly64 4.15 Na C A:Gly64 4.88 Na O A:Val65 2.60 Na N A:Val65 3.93 Na CB A:Val65 4.49 Na C A:Val65 3.63 Na CA A:Val65 4.22 Na N A:Gly66 4.66 Na CA A:Gly66 4.89 Na O3' D:Dt2 4.63 Na OP1 D:Dc3 2.70 Na P D:Dc3 3.67 Na OP2 D:Dc3 3.82 Na O5' D:Dc3 4.88 Na O A:Hoh476 2.73 Na O A:Hoh725 2.85 Na O D:Hoh164 3.65 interactive model: