Sodium in the structure of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb 1hzy)

The binding sites of Sodium atom in the structure of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1hzy). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1hzy structure was solved by H.M.HOLDEN, M.M.BENNING, F.M.RAUSHEL, H.SHIM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.3 Space group C121 a (A) 128.400 b (A) 90.030 c (A) 68.400 alpha (°) 90.00 beta (°) 91.70 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 1hzy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1hzy. 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: Asn38, A: Ile154, A: Gln155, A: Arg164, A: Ala165, A: Hoh431, A: Hoh433, A: Hoh435, A: Hoh436, A: Hoh547, A: Hoh548, A: Hoh815, A: Hoh963, conact list: Atom Atom Distance (A) Na OD1 A:Asn38 3.15 Na CG A:Asn38 4.35 Na O A:Ile154 2.72 Na CB A:Ile154 4.88 Na CG2 A:Ile154 3.76 Na C A:Ile154 3.70 Na CA A:Ile154 4.70 Na O A:Gln155 4.89 Na N A:Gln155 4.36 Na C A:Gln155 4.97 Na CA A:Gln155 4.20 Na CB A:Arg164 4.41 Na CD A:Arg164 4.19 Na CG A:Arg164 4.69 Na NH1 A:Arg164 4.99 Na O A:Ala165 4.84 Na O A:Hoh431 3.17 Na O A:Hoh433 4.81 Na O A:Hoh435 3.28 Na O A:Hoh436 2.57 Na O A:Hoh547 4.02 Na O A:Hoh548 3.93 Na O A:Hoh815 2.19 Na O A:Hoh963 2.27 interactive model: Sodium binding site 2 out of 2 in 1hzy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1hzy. 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: Asn38, B: Ile154, B: Gln155, B: Arg164, B: Ala165, B: Hoh629, B: Hoh635, B: Hoh636, B: Hoh637, B: Hoh709, B: Hoh799, B: Hoh812, B: Hoh873, conact list: Atom Atom Distance (A) Na OD1 B:Asn38 3.18 Na CG B:Asn38 4.38 Na O B:Ile154 2.53 Na CB B:Ile154 4.49 Na CG2 B:Ile154 3.38 Na C B:Ile154 3.44 Na CA B:Ile154 4.38 Na O B:Gln155 4.84 Na N B:Gln155 4.12 Na C B:Gln155 4.85 Na CA B:Gln155 4.07 Na CB B:Arg164 4.33 Na CD B:Arg164 4.36 Na CG B:Arg164 4.77 Na O B:Ala165 4.45 Na O B:Hoh629 4.90 Na O B:Hoh635 2.24 Na O B:Hoh636 3.67 Na O B:Hoh637 4.01 Na O B:Hoh709 4.49 Na O B:Hoh799 3.11 Na O B:Hoh812 2.69 Na O B:Hoh873 2.56 interactive model: