Sodium in the structure of Dna Polymerase Lambda in Complex With Arac (pdb 3mda)

The binding sites of Sodium atom in the structure of Dna Polymerase Lambda in Complex With Arac (pdb code 3mda). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3mda structure was solved by M.GARCIA-DIAZ, M.MURRAY, T.KUNKEL, K.M.CHOU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.6-2.0 Space group P212121 a (A) 56.068 b (A) 62.637 c (A) 140.163 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.7 Rfree (%) 25.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3mda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3mda. 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: Ser339, A: Asn340, A: Ile341, A: Trp342, A: Gly343, A: Ala344, A: Gly345, P: Dt4, P: Da5, A: Hoh82, A: Hoh114, A: Hoh579, P: Hoh8, P: Hoh151, P: Hoh275, conact list: Atom Atom Distance (A) Na O A:Ser339 2.56 Na CB A:Ser339 4.70 Na C A:Ser339 3.51 Na CA A:Ser339 4.21 Na O A:Asn340 4.87 Na N A:Asn340 4.42 Na C A:Asn340 4.31 Na CA A:Asn340 4.52 Na O A:Ile341 2.50 Na N A:Ile341 4.11 Na C A:Ile341 3.42 Na CA A:Ile341 4.41 Na N A:Trp342 4.07 Na C A:Trp342 4.23 Na CA A:Trp342 3.96 Na N A:Gly343 3.81 Na C A:Gly343 4.59 Na CA A:Gly343 4.73 Na O A:Ala344 2.45 Na N A:Ala344 3.70 Na C A:Ala344 3.52 Na CB A:Ala344 4.65 Na CA A:Ala344 4.15 Na N A:Gly345 4.55 Na CA A:Gly345 4.77 Na O3' P:Dt4 4.30 Na OP1 P:Da5 2.45 Na P P:Da5 3.42 Na OP2 P:Da5 3.61 Na O5' P:Da5 4.67 Na O A:Hoh82 4.76 Na O A:Hoh114 3.68 Na O A:Hoh579 2.62 Na O P:Hoh8 2.80 Na O P:Hoh151 4.00 Na O P:Hoh275 4.67 interactive model: Sodium binding site 2 out of 2 in 3mda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3mda. 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: Ser463, A: Gln464, A: Glu465, A: Glu466, T: Dt10, A: Hoh66, A: Hoh596, A: Hoh599, T: Hoh76, T: Hoh145, conact list: Atom Atom Distance (A) Na O A:Ser463 2.62 Na N A:Ser463 4.78 Na CB A:Ser463 4.50 Na C A:Ser463 3.72 Na CA A:Ser463 4.56 Na N A:Gln464 4.61 Na CA A:Gln464 4.62 Na N A:Glu465 4.47 Na OE2 A:Glu465 4.81 Na OE1 A:Glu466 4.43 Na OE2 A:Glu466 4.11 Na CD A:Glu466 4.65 Na OP1 T:Dt10 3.90 Na P T:Dt10 4.71 Na OP2 T:Dt10 4.48 Na O A:Hoh66 2.82 Na O A:Hoh596 3.93 Na O A:Hoh599 2.94 Na O T:Hoh76 2.91 Na O T:Hoh145 2.89 interactive model: