Sodium in the structure of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal (pdb 2pfq)

The binding sites of Sodium atom in the structure of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal (pdb code 2pfq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2pfq structure was solved by M.GARCIA-DIAZ, K.BEBENEK, J.M.KRAHN, L.C.PEDERSEN, T.A.KUNKEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.1 Space group P212121 a (A) 56.091 b (A) 63.485 c (A) 139.775 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 25.6 Rfree (%) 28.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2pfq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2pfq. 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: Dc6, P: Dc7, A: Asp427, A: Asp429, A: Arg488, A: Asp490, A: Mg1294, A: Mn1296, A: Mn1297, A: Dcp1438, A: Ppv1439, P: Hoh299, A: Hoh1530, conact list: Atom Atom Distance (A) Na OP1 P:Dc6 4.86 Na OP1 P:Dc6 4.82 Na C3' P:Dc6 3.28 Na C3' P:Dc6 3.65 Na O3' P:Dc6 2.00 Na O3' P:Dc6 2.49 Na C5' P:Dc6 3.95 Na C5' P:Dc6 4.26 Na C2' P:Dc6 4.40 Na C2' P:Dc6 4.93 Na C4' P:Dc6 3.69 Na C4' P:Dc6 4.30 Na O5' P:Dc6 4.59 Na O5' P:Dc6 4.61 Na OP1 P:Dc7 1.91 Na P P:Dc7 2.30 Na OP2 P:Dc7 3.27 Na C5' P:Dc7 3.97 Na O5' P:Dc7 3.60 Na CB A:Asp427 4.53 Na CB A:Asp427 4.55 Na OD2 A:Asp427 2.42 Na OD2 A:Asp427 2.26 Na OD1 A:Asp427 3.30 Na OD1 A:Asp427 3.52 Na CG A:Asp427 3.17 Na CG A:Asp427 3.22 Na CB A:Asp429 4.60 Na CB A:Asp429 4.58 Na OD2 A:Asp429 3.45 Na OD2 A:Asp429 3.58 Na OD1 A:Asp429 2.29 Na OD1 A:Asp429 2.21 Na CG A:Asp429 3.22 Na CG A:Asp429 3.24 Na NH2 A:Arg488 4.82 Na CB A:Asp490 3.80 Na CB A:Asp490 3.79 Na OD2 A:Asp490 3.93 Na OD2 A:Asp490 4.02 Na OD1 A:Asp490 1.96 Na OD1 A:Asp490 2.36 Na CG A:Asp490 3.04 Na CG A:Asp490 3.18 Na MG A:Mg1294 3.68 Na MN A:Mn1296 3.62 Na MN A:Mn1297 0.20 Na O2G A:Dcp1438 4.86 Na PA A:Dcp1438 3.47 Na O2A A:Dcp1438 2.45 Na C5' A:Dcp1438 3.93 Na O5' A:Dcp1438 3.87 Na O2B A:Dcp1438 4.80 Na O3A A:Dcp1438 4.78 Na O1A A:Dcp1438 3.89 Na O21 A:Ppv1439 4.78 Na O11 A:Ppv1439 4.84 Na O12 A:Ppv1439 4.73 Na O P:Hoh299 2.30 Na O A:Hoh1530 4.30 interactive model: Sodium binding site 2 out of 2 in 2pfq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2pfq. 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: Dt4, P: Da5, A: Ser339, A: Asn340, A: Ile341, A: Trp342, A: Gly343, A: Ala344, A: Gly345, A: Hoh1452, A: Hoh1463, A: Hoh1471, A: Hoh1482, A: Hoh1485, conact list: Atom Atom Distance (A) Na O3' P:Dt4 4.47 Na OP1 P:Da5 2.39 Na P P:Da5 3.48 Na OP2 P:Da5 3.70 Na O5' P:Da5 4.65 Na O A:Ser339 2.43 Na C A:Ser339 3.52 Na CA A:Ser339 4.36 Na O A:Asn340 4.92 Na N A:Asn340 4.41 Na C A:Asn340 4.25 Na CA A:Asn340 4.48 Na O A:Ile341 2.45 Na N A:Ile341 3.87 Na C A:Ile341 3.36 Na CA A:Ile341 4.32 Na N A:Trp342 4.03 Na C A:Trp342 4.34 Na CA A:Trp342 3.98 Na N A:Gly343 4.06 Na C A:Gly343 4.74 Na O A:Ala344 2.26 Na N A:Ala344 3.76 Na C A:Ala344 3.41 Na CB A:Ala344 4.56 Na CA A:Ala344 4.10 Na N A:Gly345 4.46 Na CA A:Gly345 4.68 Na O A:Hoh1452 2.51 Na O A:Hoh1463 4.72 Na O A:Hoh1471 3.93 Na O A:Hoh1482 4.68 Na O A:Hoh1485 4.45 interactive model: