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Sodium in PDB 1i0d: High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta

Enzymatic activity of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta

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

Protein crystallography data

The structure of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0d 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 (°) 128.444, 90.034, 68.385, 90.00, 91.72, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1i0d:

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

Cadmium (Cd) 2 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1i0d). 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/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1i0d

Go back to Sodium Binding Sites List in 1i0d
Sodium binding site 1 out of 2 in the High Resolution Structure of the Zinc/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 Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:41.3
occ:1.00
O A:HOH1063 2.2 29.2 1.0
O A:HOH796 2.3 19.9 1.0
O A:HOH1058 2.3 26.5 1.0
O A:ILE154 2.7 10.9 1.0
O A:HOH422 3.1 14.5 1.0
OD1 A:ASN38 3.2 27.9 1.0
O A:HOH426 3.6 23.0 1.0
CG2 A:ILE154 3.6 12.8 1.0
C A:ILE154 3.6 11.1 1.0
O A:HOH542 3.9 17.2 1.0
O A:HOH541 4.2 17.5 1.0
CA A:GLN155 4.2 11.3 1.0
CD A:ARG164 4.2 14.7 1.0
N A:GLN155 4.3 11.3 1.0
CG A:ASN38 4.4 12.7 1.0
CB A:ARG164 4.4 12.7 1.0
CA A:ILE154 4.6 9.2 1.0
CB A:ILE154 4.7 9.8 1.0
O A:ALA165 4.8 10.6 1.0
CG A:ARG164 4.8 11.6 1.0
O A:HOH424 4.9 22.6 1.0

Sodium binding site 2 out of 2 in 1i0d

Go back to Sodium Binding Sites List in 1i0d
Sodium binding site 2 out of 2 in the High Resolution Structure of the Zinc/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 Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:39.6
occ:1.00
O B:HOH1062 2.3 29.1 1.0
O B:ILE154 2.5 14.1 1.0
O B:HOH794 2.6 18.4 1.0
O B:HOH818 2.6 29.4 1.0
OD1 B:ASN38 3.1 35.9 1.0
O B:HOH788 3.1 17.0 1.0
C B:ILE154 3.4 12.6 1.0
CG2 B:ILE154 3.5 14.8 1.0
O B:HOH628 3.6 19.5 1.0
O B:HOH629 4.0 20.2 1.0
CA B:GLN155 4.0 12.6 1.0
N B:GLN155 4.1 13.8 1.0
CD B:ARG164 4.2 14.2 1.0
CB B:ARG164 4.3 13.1 1.0
CG B:ASN38 4.3 15.0 1.0
O B:HOH702 4.3 19.9 1.0
CA B:ILE154 4.4 11.4 1.0
O B:ALA165 4.5 12.3 1.0
CB B:ILE154 4.6 11.5 1.0
CG B:ARG164 4.7 11.6 1.0
O B:GLN155 4.8 17.5 1.0
C B:GLN155 4.8 14.4 1.0
O B:HOH622 4.9 22.4 1.0

Reference:

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
Page generated: Tue Dec 15 05:25:38 2020

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