Sodium in the structure of Crystal Structure Of the Pre-Catalytic Ternary Complex of Polymerase Lambda With An Ratp Analog Opposite A Templating T. (pdb 3upq)

The binding sites of Sodium atom in the structure of Crystal Structure Of the Pre-Catalytic Ternary Complex of Polymerase Lambda With An Ratp Analog Opposite A Templating T. (pdb code 3upq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3upq structure was solved by R.A.GOSAVI, A.F.MOON, T.A.KUNKEL, L.C.PEDERSEN, K.BEBENEK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 27.4-1.9 Space group P212121 a (A) 55.975 b (A) 63.660 c (A) 139.970 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.8 Rfree (%) 24.4 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3upq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3upq. 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: Hoh578, P: Hoh47, P: Hoh50, conact list: Atom Atom Distance (A) Na O A:Ser339 2.44 Na CB A:Ser339 4.97 Na C A:Ser339 3.55 Na CA A:Ser339 4.40 Na O A:Asn340 4.81 Na N A:Asn340 4.45 Na C A:Asn340 4.30 Na CA A:Asn340 4.45 Na O A:Ile341 2.62 Na N A:Ile341 4.21 Na C A:Ile341 3.47 Na CA A:Ile341 4.51 Na N A:Trp342 4.03 Na C A:Trp342 4.26 Na CA A:Trp342 3.88 Na N A:Gly343 3.88 Na C A:Gly343 4.71 Na CA A:Gly343 4.84 Na O A:Ala344 2.56 Na N A:Ala344 3.80 Na C A:Ala344 3.64 Na CB A:Ala344 4.84 Na CA A:Ala344 4.28 Na N A:Gly345 4.66 Na CA A:Gly345 4.90 Na O3' P:Dt4 4.46 Na OP1 P:Da5 2.49 Na P P:Da5 3.52 Na OP2 P:Da5 3.65 Na O5' P:Da5 4.76 Na O A:Hoh578 2.41 Na O P:Hoh47 3.94 Na O P:Hoh50 2.60 interactive model: