Sodium in PDB 1hzy: High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta

All present enzymatic activity of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta:
3.1.8.1;

The structure of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1hzy was solved by H.M.Holden, M.M.Benning, F.M.Raushel, H.Shim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.400, 90.030, 68.400, 90.00, 91.70, 90.00
R / Rfree (%)	n/a / n/a

The structure of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1hzy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1hzy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:40.7 occ:1.00 O A:HOH815 2.2 20.4 1.0 O A:HOH963 2.3 28.6 1.0 O A:HOH436 2.6 34.9 1.0 O A:ILE154 2.7 9.8 1.0 OD1 A:ASN38 3.1 23.9 1.0 O A:HOH431 3.2 14.6 1.0 O A:HOH435 3.3 18.1 1.0 C A:ILE154 3.7 11.1 1.0 CG2 A:ILE154 3.8 12.0 1.0 O A:HOH548 3.9 17.4 1.0 O A:HOH547 4.0 17.6 1.0 CD A:ARG164 4.2 16.7 1.0 CA A:GLN155 4.2 12.2 1.0 CG A:ASN38 4.3 11.3 1.0 N A:GLN155 4.4 13.3 1.0 CB A:ARG164 4.4 12.6 1.0 CG A:ARG164 4.7 12.9 1.0 CA A:ILE154 4.7 9.1 1.0 O A:HOH433 4.8 21.0 1.0 O A:ALA165 4.8 11.1 1.0 CB A:ILE154 4.9 11.0 1.0 O A:GLN155 4.9 14.5 1.0 C A:GLN155 5.0 11.7 1.0 NH1 A:ARG164 5.0 16.8 1.0

Sodium binding site 2 out of 2 in the High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Structure of the Zinc-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:37.5 occ:1.00 O B:HOH635 2.2 34.9 1.0 O B:ILE154 2.5 13.4 1.0 O B:HOH873 2.6 29.7 1.0 O B:HOH812 2.7 17.5 1.0 O B:HOH799 3.1 18.0 1.0 OD1 B:ASN38 3.2 34.7 1.0 CG2 B:ILE154 3.4 13.6 1.0 C B:ILE154 3.4 13.3 1.0 O B:HOH636 3.7 17.7 1.0 O B:HOH637 4.0 18.5 1.0 CA B:GLN155 4.1 11.0 1.0 N B:GLN155 4.1 13.3 1.0 CB B:ARG164 4.3 12.3 1.0 CD B:ARG164 4.4 13.6 1.0 CA B:ILE154 4.4 9.9 1.0 CG B:ASN38 4.4 16.6 1.0 O B:ALA165 4.4 12.2 1.0 CB B:ILE154 4.5 10.9 1.0 O B:HOH709 4.5 16.4 1.0 CG B:ARG164 4.8 9.9 1.0 O B:GLN155 4.8 15.6 1.0 C B:GLN155 4.8 11.9 1.0 O B:HOH629 4.9 19.2 1.0

M.M.Benning, H.Shim, F.M.Raushel, H.M.Holden. High Resolution X-Ray Structures of Different Metal-Substituted Forms of Phosphotriesterase From Pseudomonas Diminuta. Biochemistry V. 40 2712 2001.
ISSN: ISSN 0006-2960
PubMed: 11258882
DOI: 10.1021/BI002661E