Sodium in PDB 7cuf: Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution

All present enzymatic activity of Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution:
1.7.3.3;

The structure of Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution, PDB code: 7cuf was solved by T.Hibi, T.Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.14 / 1.46
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.622, 133.850, 145.391, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.1

The binding sites of Sodium atom in the Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution (pdb code 7cuf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution, PDB code: 7cuf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:35.6 occ:1.00 HB A:THR31 2.5 37.0 1.0 O A:ILE32 2.7 30.4 1.0 O A:HOH664 2.9 31.2 1.0 O A:SER35 3.0 26.6 1.0 HG1 A:THR31 3.1 41.3 1.0 CB A:THR31 3.3 30.8 1.0 OG1 A:THR31 3.4 34.4 1.0 HA A:PRO33 3.4 39.2 1.0 C A:ILE32 3.5 29.2 1.0 H A:ILE32 3.6 37.8 1.0 N A:ILE32 3.8 31.5 1.0 HA A:PRO36 3.8 34.2 1.0 HG21 A:THR31 3.9 36.2 1.0 C A:SER35 4.1 28.4 1.0 N A:PRO33 4.2 33.1 1.0 CA A:PRO33 4.2 32.7 1.0 CG2 A:THR31 4.2 30.2 1.0 O A:HOH594 4.2 26.6 1.0 CA A:ILE32 4.2 33.4 1.0 C A:THR31 4.2 32.2 1.0 H A:SER35 4.3 32.4 1.0 CA A:THR31 4.4 36.6 1.0 HA A:ILE32 4.6 40.0 1.0 HG22 A:THR31 4.6 36.2 1.0 CA A:PRO36 4.6 28.5 1.0 HA A:THR31 4.6 43.9 1.0 C A:PRO33 4.7 29.6 1.0 O A:PRO33 4.8 30.5 1.0 N A:PRO36 4.8 26.6 1.0 N A:SER35 4.9 27.0 1.0 HG23 A:THR31 5.0 36.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Urate Oxidase From Bacillus Sp. Tb-90 in the Absence From Chloride Anion at 1.44 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:23.9 occ:1.00 OG B:SER38 2.7 18.6 1.0 O B:HOH607 2.9 16.9 1.0 HB2 B:SER38 3.0 19.8 1.0 CB B:SER38 3.4 16.5 1.0 HG B:SER38 3.4 22.3 1.0 O B:SER38 3.7 13.6 1.0 HB3 B:SER38 4.0 19.8 1.0 C B:SER38 4.2 13.5 1.0 CA B:SER38 4.4 15.7 1.0 HG1 B:THR27 4.4 20.7 1.0 O B:HOH545 4.7 33.0 1.0 HA B:SER38 5.0 18.8 1.0

T.Hibi, T.Itoh. Identification of Quasi-Stable Water Molecules Near the THR73-LYS13 Catalytic Diad of Bacillus Sp. Tb-90 Urate Oxidase By X-Ray Crystallography with Controlled Humidity. J.Biochem. 2020.
ISSN: ISSN 0021-924X
PubMed: 33002140
DOI: 10.1093/JB/MVAA114