Sodium in the structure of Crystal Structure of Ribose-5-Isomerase A (pdb 3kwm)

The binding sites of Sodium atom in the structure of Crystal Structure of Ribose-5-Isomerase A (pdb code 3kwm). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3kwm structure was solved by M.ORLIKOWSKA, R.ROSTANKOWSKI, C.NAKKA, J.HATTNE, S.GRIMSHAW, D.BOREK, Z.OTWINOWSKI, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES(CSGID), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.7-2.3 Space group P21212 a (A) 182.360 b (A) 73.085 c (A) 75.303 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 22.1 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3kwm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3kwm. 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: Asn193, A: Val198, A: Val199, A: Thr200, D: Asn193, D: Val198, D: Val199, A: Hoh230, A: Hoh241, D: Hoh234, D: Hoh267, conact list: Atom Atom Distance (A) Na O A:Asn193 4.68 Na O A:Val198 2.77 Na C A:Val198 3.83 Na O A:Val199 3.11 Na N A:Val199 4.33 Na C A:Val199 3.78 Na CA A:Val199 3.90 Na N A:Thr200 4.92 Na O D:Asn193 4.58 Na O D:Val198 2.54 Na C D:Val198 3.66 Na CA D:Val198 4.82 Na O D:Val199 3.39 Na N D:Val199 4.30 Na C D:Val199 4.00 Na CA D:Val199 4.05 Na O A:Hoh230 3.87 Na O A:Hoh241 2.30 Na O D:Hoh234 2.49 Na O D:Hoh267 4.13 interactive model: Sodium binding site 2 out of 2 in 3kwm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3kwm. 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: B: Asn193, B: Val198, B: Val199, B: Thr200, C: Asn193, C: Val198, C: Val199, B: Hoh231, C: Hoh255, conact list: Atom Atom Distance (A) Na O B:Asn193 4.85 Na O B:Val198 2.68 Na C B:Val198 3.78 Na O B:Val199 3.05 Na N B:Val199 4.31 Na C B:Val199 3.80 Na CA B:Val199 3.92 Na N B:Thr200 4.97 Na O C:Asn193 4.79 Na O C:Val198 2.70 Na C C:Val198 3.81 Na CA C:Val198 4.99 Na O C:Val199 3.08 Na N C:Val199 4.40 Na C C:Val199 3.87 Na CA C:Val199 4.02 Na O B:Hoh231 4.14 Na O C:Hoh255 3.96 interactive model: