Sodium in PDB 7cuc: 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: 7cuc 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)	37.87 / 1.44
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.618, 133.836, 145.363, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.8

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 7cuc). 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: 7cuc:
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:55.5 occ:1.00 HB A:THR31 2.5 36.9 1.0 O A:ILE32 2.5 37.4 1.0 O A:HOH720 2.9 38.1 1.0 O A:SER35 3.0 29.2 1.0 HG1 A:THR31 3.2 46.3 1.0 C A:ILE32 3.3 34.4 1.0 CB A:THR31 3.3 30.8 1.0 HA A:PRO33 3.4 44.0 1.0 OG1 A:THR31 3.5 38.6 1.0 H A:ILE32 3.5 44.0 1.0 N A:ILE32 3.7 36.6 1.0 HA A:PRO36 4.0 38.0 1.0 HG21 A:THR31 4.0 36.8 1.0 O A:HOH589 4.0 28.6 1.0 N A:PRO33 4.1 38.0 1.0 CA A:PRO33 4.1 36.7 1.0 CA A:ILE32 4.1 38.6 1.0 H A:SER35 4.1 34.6 1.0 C A:SER35 4.1 29.9 1.0 C A:THR31 4.2 39.4 1.0 CG2 A:THR31 4.2 30.7 1.0 CA A:THR31 4.3 42.6 1.0 HA A:ILE32 4.5 46.3 1.0 C A:PRO33 4.6 34.4 1.0 HA A:THR31 4.6 51.1 1.0 HG22 A:THR31 4.6 36.8 1.0 O A:PRO33 4.6 32.9 1.0 CA A:PRO36 4.7 31.7 1.0 N A:SER35 4.8 28.8 1.0 HG13 A:ILE32 4.9 45.1 1.0 N A:PRO36 4.9 28.4 1.0 O A:THR31 5.0 31.8 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:Na406 b:27.6 occ:1.00 O B:HOH811 2.5 25.5 1.0 OG B:SER38 2.8 20.7 1.0 O B:HOH589 2.9 18.7 1.0 HB2 B:SER38 2.9 21.4 1.0 CB B:SER38 3.4 17.8 1.0 HG B:SER38 3.5 24.8 1.0 O B:SER38 3.7 16.2 1.0 O B:HOH761 3.8 40.5 1.0 HB3 B:SER38 4.0 21.4 1.0 C B:SER38 4.2 14.6 1.0 HG1 B:THR27 4.4 23.0 1.0 CA B:SER38 4.4 16.4 1.0 O B:HOH543 4.6 37.4 1.0 HA B:SER38 4.9 19.6 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