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

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

The structure of High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1jgm was solved by M.M.Benning, H.Shim, F.M.Raushel, H.M.Holden, 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 (°)	128.450, 90.030, 68.390, 90.00, 91.72, 90.00
R / Rfree (%)	20.2 / 23.6

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

Cadmium

(Cd)

4 atoms

The binding sites of Sodium atom in the High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1jgm). 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 Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1jgm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High Resolution Structure of the Cadmium-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 Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5 b:43.0 occ:1.00 O A:HOH376 2.2 26.6 1.0 O A:HOH557 2.4 18.9 1.0 O A:HOH615 2.4 28.9 1.0 O A:ILE154 2.7 11.2 1.0 O A:HOH371 3.0 13.8 1.0 OD1 A:ASN38 3.1 29.0 1.0 O A:HOH375 3.5 21.1 1.0 CG2 A:ILE154 3.6 14.0 1.0 C A:ILE154 3.7 11.4 1.0 O A:HOH475 3.9 16.4 1.0 CG A:ASN38 4.3 13.5 1.0 CD A:ARG164 4.3 15.8 1.0 CA A:GLN155 4.3 12.0 1.0 CB A:ARG164 4.4 14.1 1.0 N A:GLN155 4.4 11.6 1.0 O A:HOH474 4.4 17.9 1.0 CA A:ILE154 4.6 10.8 1.0 O A:ALA165 4.6 11.8 1.0 O A:HOH373 4.7 20.6 1.0 CB A:ILE154 4.7 11.4 1.0 O A:HOH668 4.8 42.8 1.0 CG A:ARG164 4.8 13.2 1.0

Sodium binding site 2 out of 2 in the High Resolution Structure of the Cadmium-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 Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na6 b:44.6 occ:1.00 O B:HOH391 2.0 25.2 1.0 O B:ILE154 2.4 14.2 1.0 O B:HOH593 2.7 39.6 1.0 O B:HOH566 2.8 19.7 1.0 O B:HOH559 3.0 16.9 1.0 OD1 B:ASN38 3.1 30.2 1.0 C B:ILE154 3.4 13.5 1.0 CG2 B:ILE154 3.4 15.1 1.0 O B:HOH392 3.7 20.0 1.0 O B:HOH393 4.0 20.8 1.0 N B:GLN155 4.1 14.8 1.0 CA B:GLN155 4.1 13.4 1.0 CD B:ARG164 4.2 15.1 1.0 CG B:ASN38 4.3 15.4 1.0 CB B:ARG164 4.3 13.7 1.0 CA B:ILE154 4.3 11.3 1.0 O B:ALA165 4.4 13.6 1.0 CB B:ILE154 4.5 12.3 1.0 O B:HOH468 4.6 19.5 1.0 CG B:ARG164 4.7 13.9 1.0 O B:GLN155 4.9 16.7 1.0 C B:GLN155 4.9 14.6 1.0 O B:HOH385 4.9 22.3 1.0 CG1 B:VAL196 4.9 10.5 0.5

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