Sodium in the structure of Dna Polymerase Beta With A Terminated Gapped Dna Substrate and Ddctp With Sodium in the Catalytic Site (pdb 2fmp)

The binding sites of Sodium atom in the structure of Dna Polymerase Beta With A Terminated Gapped Dna Substrate and Ddctp With Sodium in the Catalytic Site (pdb code 2fmp). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2fmp structure was solved by V.K.BATRA, W.A.BEARD, D.D.SHOCK, J.M.KRAHN, L.C.PEDERSEN, S.H.WILSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 17.2-1.6 Space group P1211 a (A) 50.900 b (A) 80.400 c (A) 55.300 alpha (°) 90.00 beta (°) 107.50 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 21.7 Sodium Binding Sites: Sodium binding site 1 out of 5 in 2fmp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2fmp. 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: Mg1339, A: Dct1338, P: Hoh11, A: Hoh1408, A: Hoh1453, A: Hoh1568, conact list: Atom Atom Distance (A) Na OP1 P:Doc10 4.82 Na C3' P:Doc10 3.72 Na C5' P:Doc10 4.22 Na C4' P:Doc10 4.30 Na O5' P:Doc10 4.86 Na CB A:Asp190 4.30 Na OD2 A:Asp190 2.26 Na OD1 A:Asp190 2.89 Na CG A:Asp190 2.89 Na O A:Met191 4.76 Na O A:Met191 4.48 Na C A:Met191 4.95 Na C A:Met191 4.87 Na CB A:Asp192 4.52 Na OD2 A:Asp192 3.47 Na OD1 A:Asp192 2.22 Na CG A:Asp192 3.19 Na CA A:Asp192 4.94 Na NH2 A:Arg254 4.94 Na CB A:Asp256 4.15 Na OD2 A:Asp256 2.38 Na OD1 A:Asp256 4.55 Na CG A:Asp256 3.54 Na MG A:Mg1339 3.44 Na PA A:Dct1338 3.61 Na O2A A:Dct1338 4.21 Na C5' A:Dct1338 4.03 Na O5' A:Dct1338 3.84 Na O2B A:Dct1338 4.99 Na O3A A:Dct1338 4.95 Na O1G A:Dct1338 4.57 Na O1A A:Dct1338 2.48 Na O P:Hoh11 2.52 Na O A:Hoh1408 4.55 Na O A:Hoh1453 4.28 Na O A:Hoh1568 4.81 interactive model: Sodium binding site 2 out of 5 in 2fmp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2fmp. 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: Hoh12, P: Hoh24, A: Hoh1410, A: Hoh1720, A: Hoh1838, A: Hoh1895, conact list: Atom Atom Distance (A) Na O3' P:Dc8 4.46 Na OP1 P:Dg9 2.65 Na P P:Dg9 3.63 Na OP2 P:Dg9 3.73 Na O5' P:Dg9 4.91 Na O A:Leu100 4.94 Na O A:Thr101 2.41 Na CB A:Thr101 4.50 Na C A:Thr101 3.37 Na CA A:Thr101 3.96 Na O A:Arg102 4.84 Na N A:Arg102 4.39 Na C A:Arg102 4.37 Na CA A:Arg102 4.66 Na O A:Val103 2.51 Na N A:Val103 4.13 Na C A:Val103 3.48 Na CA A:Val103 4.48 Na N A:Ser104 4.13 Na C A:Ser104 4.33 Na CA A:Ser104 4.01 Na N A:Gly105 3.96 Na C A:Gly105 4.66 Na CA A:Gly105 4.90 Na O A:Ile106 2.48 Na N A:Ile106 3.78 Na CB A:Ile106 4.57 Na C A:Ile106 3.52 Na CA A:Ile106 4.17 Na N A:Gly107 4.50 Na CA A:Gly107 4.74 Na O P:Hoh12 2.31 Na O P:Hoh24 4.24 Na O A:Hoh1410 2.45 Na O A:Hoh1720 4.80 Na O A:Hoh1838 4.10 Na O A:Hoh1895 4.90 interactive model: Sodium binding site 3 out of 5 in 2fmp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2fmp. 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: Hoh6, D: Hoh14, A: Hoh1411, conact list: Atom Atom Distance (A) Na O3' D:Dt2 4.52 Na OP1 D:Dc3 2.68 Na OP1 D:Dc3 2.58 Na P D:Dc3 3.60 Na P D:Dc3 3.71 Na OP2 D:Dc3 3.65 Na OP2 D:Dc3 4.00 Na O5' D:Dc3 4.87 Na O5' D:Dc3 4.95 Na O A:Ala59 4.86 Na O A:Lys60 2.33 Na CB A:Lys60 4.89 Na C A:Lys60 3.44 Na CG A:Lys60 4.35 Na CA A:Lys60 4.18 Na O A:Lys61 4.38 Na N A:Lys61 4.41 Na C A:Lys61 4.12 Na CA A:Lys61 4.57 Na O A:Leu62 2.34 Na N A:Leu62 4.00 Na C A:Leu62 3.36 Na CA A:Leu62 4.31 Na N A:Pro63 4.13 Na C A:Pro63 4.52 Na CA A:Pro63 4.12 Na N A:Gly64 4.10 Na C A:Gly64 4.81 Na O A:Val65 2.40 Na N A:Val65 3.80 Na CB A:Val65 4.34 Na C A:Val65 3.50 Na CA A:Val65 4.12 Na N A:Gly66 4.58 Na CA A:Gly66 4.88 Na O D:Hoh6 2.60 Na O D:Hoh14 4.01 Na O A:Hoh1411 2.42 interactive model: Sodium binding site 4 out of 5 in 2fmp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2fmp. 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: Arg126, A: Lys127, A: Glu129, A: Na1406, A: Hoh1459, A: Hoh1493, A: Hoh1501, A: Hoh1510, A: Hoh1526, A: Hoh1528, A: Hoh1569, A: Hoh1614, conact list: Atom Atom Distance (A) Na O A:Arg126 2.59 Na CB A:Arg126 4.43 Na C A:Arg126 3.67 Na CA A:Arg126 4.61 Na N A:Lys127 4.44 Na CB A:Lys127 4.86 Na CA A:Lys127 4.36 Na OE1 A:Glu129 4.28 Na OE1 A:Glu129 4.80 Na OE2 A:Glu129 3.96 Na CD A:Glu129 4.72 Na NA A:Na1406 3.21 Na O A:Hoh1459 4.04 Na O A:Hoh1493 2.43 Na O A:Hoh1501 2.48 Na O A:Hoh1510 2.45 Na O A:Hoh1526 2.30 Na O A:Hoh1528 4.62 Na O A:Hoh1569 2.33 Na O A:Hoh1614 3.96 interactive model: Sodium binding site 5 out of 5 in 2fmp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2fmp. 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: Glu129, A: Na1402, A: Hoh1459, A: Hoh1493, A: Hoh1499, A: Hoh1501, A: Hoh1504, A: Hoh1510, A: Hoh1526, A: Hoh1528, A: Hoh1558, conact list: Atom Atom Distance (A) Na OE1 A:Glu129 4.55 Na OE2 A:Glu129 4.49 Na NA A:Na1402 3.21 Na O A:Hoh1459 4.14 Na O A:Hoh1493 4.97 Na O A:Hoh1499 2.39 Na O A:Hoh1501 2.47 Na O A:Hoh1504 4.24 Na O A:Hoh1510 2.67 Na O A:Hoh1526 2.47 Na O A:Hoh1528 2.29 Na O A:Hoh1558 2.39 interactive model: