Sodium in the structure of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant With Substrate (pdb 3a65)

The binding sites of Sodium atom in the structure of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant With Substrate (pdb code 3a65). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3a65 structure was solved by Y.KAWASHIMA, N.SHIBATA, Y.HIGUCHI, M.TAKEO, S.NEGORO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.6-1.7 Space group P3221 a (A) 96.414 b (A) 96.414 c (A) 112.869 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18 Rfree (%) 20.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3a65 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3a65. 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: Gly123, A: Ala124, A: Val126, A: Asp127, A: Val295, A: Ser296, A: Trp299, A: Hoh434, A: Hoh639, A: Hoh643, conact list: Atom Atom Distance (A) Na O A:Gly123 2.83 Na C A:Gly123 3.57 Na CA A:Gly123 4.07 Na N A:Ala124 4.51 Na CA A:Ala124 4.87 Na CB A:Val126 4.87 Na N A:Asp127 4.22 Na CB A:Asp127 3.86 Na OD2 A:Asp127 2.23 Na OD1 A:Asp127 2.24 Na CG A:Asp127 2.45 Na CA A:Asp127 4.42 Na CB A:Val295 3.78 Na C A:Val295 4.06 Na CG1 A:Val295 4.22 Na CA A:Val295 4.01 Na O A:Ser296 4.57 Na N A:Ser296 3.16 Na CB A:Ser296 3.65 Na OG A:Ser296 3.02 Na C A:Ser296 4.72 Na CA A:Ser296 3.97 Na N A:Trp299 4.47 Na CB A:Trp299 2.96 Na CD1 A:Trp299 4.46 Na CD2 A:Trp299 3.85 Na CE3 A:Trp299 3.92 Na CG A:Trp299 3.50 Na CA A:Trp299 4.25 Na CE2 A:Trp299 4.93 Na O A:Hoh434 4.81 Na O A:Hoh639 4.53 Na O A:Hoh643 2.94 interactive model: