Sodium in the structure of Phosphoribosylamine-Glycine Ligase From Yersinia Pestis (pdb 3mjf)

The binding sites of Sodium atom in the structure of Phosphoribosylamine-Glycine Ligase From Yersinia Pestis (pdb code 3mjf). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3mjf structure was solved by J.OSIPIUK, M.ZHOU, L.PAPAZISI, W.F.ANDERSON, A.JOACHIMIAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.8-1.5 Space group P212121 a (A) 68.637 b (A) 69.151 c (A) 95.166 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.5 Rfree (%) 17.4 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3mjf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3mjf. 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: Asp214, A: Lys216, A: Gly228, A: Gly229, A: Arg290, A: Phe291, A: Gly292, A: Asp293, A: Pro294, A: Glu295, A: Arg383, A: Hoh583, conact list: Atom Atom Distance (A) Na CB A:Asp214 4.39 Na OD2 A:Asp214 2.37 Na OD1 A:Asp214 4.12 Na CG A:Asp214 3.47 Na CE A:Lys216 3.79 Na CD A:Lys216 4.49 Na NZ A:Lys216 3.57 Na O A:Gly228 2.48 Na C A:Gly228 3.65 Na CA A:Gly228 4.83 Na N A:Gly229 4.26 Na CA A:Gly229 3.97 Na O A:Arg290 2.08 Na CB A:Arg290 4.71 Na CB A:Arg290 4.72 Na C A:Arg290 3.33 Na CA A:Arg290 4.32 Na CA A:Arg290 4.32 Na N A:Phe291 4.19 Na C A:Phe291 4.51 Na CA A:Phe291 4.20 Na N A:Gly292 4.53 Na C A:Gly292 4.98 Na O A:Asp293 2.47 Na N A:Asp293 3.97 Na C A:Asp293 3.20 Na CA A:Asp293 4.26 Na N A:Pro294 3.65 Na CD A:Pro294 3.41 Na CG A:Pro294 4.83 Na CA A:Pro294 5.00 Na N A:Glu295 4.84 Na OE1 A:Glu295 2.51 Na OE2 A:Glu295 3.26 Na CD A:Glu295 3.26 Na CG A:Glu295 4.69 Na NH1 A:Arg383 4.48 Na O A:Hoh583 4.03 interactive model: