Sodium in PDB 1i0b: High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta

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

The structure of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0b 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

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

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1i0b). 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 Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High Resolution Structure of the Manganese-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 Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:61.1 occ:1.00 O A:ILE154 2.1 11.6 1.0 O A:HOH787 2.4 28.9 1.0 O A:HOH1014 2.7 34.8 1.0 C A:ILE154 3.1 11.6 1.0 O A:HOH1019 3.1 29.3 1.0 CD A:ARG164 3.2 15.6 1.0 O A:HOH439 3.2 21.9 1.0 OD1 A:ASN38 3.3 28.9 1.0 CA A:GLN155 3.6 19.2 1.0 CB A:ARG164 3.6 15.1 1.0 CG A:ARG164 3.6 22.1 1.0 N A:GLN155 3.8 12.5 1.0 O A:HOH545 3.8 20.8 1.0 O A:GLN155 3.9 19.0 1.0 CG2 A:ILE154 4.0 13.3 1.0 C A:GLN155 4.1 17.7 1.0 O A:HOH435 4.1 16.8 1.0 NE A:ARG164 4.2 38.0 1.0 CA A:ILE154 4.3 13.0 1.0 CG A:ASN38 4.4 22.8 1.0 NH1 A:ARG164 4.6 16.4 1.0 CB A:ILE154 4.8 14.5 1.0 CB A:GLN155 4.8 16.4 1.0 CZ A:ARG164 4.8 77.2 1.0 O A:ALA165 4.9 14.8 1.0 O A:HOH546 4.9 22.0 1.0 CA A:ARG164 4.9 14.7 1.0

Sodium binding site 2 out of 2 in the High Resolution Structure of the Manganese-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 Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:65.1 occ:1.00 O B:ILE154 2.0 17.6 1.0 O B:HOH1018 2.5 45.8 1.0 O B:HOH785 2.6 24.8 1.0 C B:ILE154 2.9 22.6 1.0 O B:HOH806 3.1 34.4 1.0 OD1 B:ASN38 3.3 38.1 1.0 CA B:GLN155 3.4 17.6 1.0 N B:GLN155 3.5 20.0 1.0 CG2 B:ILE154 3.5 13.6 1.0 CD B:ARG164 3.7 17.3 1.0 O B:HOH626 3.7 24.8 1.0 O B:HOH779 3.8 20.8 1.0 CB B:ARG164 3.9 17.5 1.0 CA B:ILE154 4.0 14.9 1.0 O B:GLN155 4.1 23.7 1.0 O B:HOH697 4.1 14.2 1.0 C B:GLN155 4.1 20.1 1.0 CG B:ARG164 4.1 15.8 1.0 CB B:ILE154 4.4 10.8 1.0 CG B:ASN38 4.5 28.8 1.0 O B:ALA165 4.6 14.9 1.0 NE B:ARG164 4.6 17.1 1.0 CB B:GLN155 4.6 19.7 1.0 CG B:GLN155 4.7 13.4 1.0 O B:HOH627 4.9 30.2 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