Sodium in the structure of Crystal Structure of A Probable Acetyltransferases (Gnat Family) From Chromobacterium Violaceum Atcc 12472 (pdb 3pzj)

The binding sites of Sodium atom in the structure of Crystal Structure of A Probable Acetyltransferases (Gnat Family) From Chromobacterium Violaceum Atcc 12472 (pdb code 3pzj). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3pzj structure was solved by B.NOCEK, A.STEIN, L.BIGELOW, B.FELDMANN, A.JOACHIMIAK, MIDWEST CENTER FORSTRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.9 Space group P212121 a (A) 64.665 b (A) 67.434 c (A) 85.271 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 24.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3pzj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3pzj. 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: Thr82, A: Val83, A: Ala84, A: Gln85, A: Ser86, A: Asp87, A: Thr88, A: Ala89, A: Hoh239, A: Hoh257, A: Hoh278, conact list: Atom Atom Distance (A) Na O A:Thr82 4.81 Na O A:Val83 2.19 Na CB A:Val83 4.79 Na C A:Val83 3.32 Na CG1 A:Val83 4.24 Na CA A:Val83 4.04 Na O A:Ala84 4.31 Na N A:Ala84 4.33 Na C A:Ala84 4.06 Na CA A:Ala84 4.47 Na O A:Gln85 2.35 Na N A:Gln85 4.08 Na C A:Gln85 3.42 Na CA A:Gln85 4.35 Na O A:Ser86 4.46 Na N A:Ser86 4.26 Na C A:Ser86 4.31 Na CA A:Ser86 4.21 Na N A:Asp87 4.85 Na O A:Thr88 2.23 Na N A:Thr88 4.09 Na CB A:Thr88 4.60 Na C A:Thr88 3.46 Na CA A:Thr88 4.25 Na N A:Ala89 4.49 Na CA A:Ala89 4.67 Na O A:Hoh239 4.89 Na O A:Hoh257 2.43 Na O A:Hoh278 2.33 interactive model: Sodium binding site 2 out of 2 in 3pzj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3pzj. 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: Val83, B: Ala84, B: Gln85, B: Ser86, B: Asp87, B: Thr88, B: Ala89, B: Hoh212, B: Hoh234, B: Hoh235, conact list: Atom Atom Distance (A) Na O B:Val83 2.40 Na CB B:Val83 4.70 Na C B:Val83 3.47 Na CG1 B:Val83 4.06 Na CA B:Val83 4.07 Na O B:Ala84 4.65 Na N B:Ala84 4.48 Na C B:Ala84 4.29 Na CA B:Ala84 4.67 Na O B:Gln85 2.30 Na N B:Gln85 4.18 Na C B:Gln85 3.45 Na CA B:Gln85 4.45 Na CA B:Gln85 4.44 Na O B:Ser86 4.24 Na N B:Ser86 4.28 Na C B:Ser86 4.31 Na CA B:Ser86 4.27 Na N B:Asp87 4.92 Na O B:Thr88 2.19 Na N B:Thr88 4.06 Na CB B:Thr88 4.61 Na C B:Thr88 3.42 Na CA B:Thr88 4.24 Na N B:Ala89 4.41 Na CA B:Ala89 4.64 Na O B:Hoh212 4.73 Na O B:Hoh234 2.56 Na O B:Hoh235 2.64 interactive model: