Sodium in PDB 2i2s: Crystal Structure of the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain

The structure of Crystal Structure of the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain, PDB code: 2i2s was solved by H.Blanchard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.929, 64.663, 109.886, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 22

The binding sites of Sodium atom in the Crystal Structure of the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain (pdb code 2i2s). 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 the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain, PDB code: 2i2s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain


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 the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6000 b:19.6 occ:1.00 OH A:TYR165 2.3 18.4 1.0 O A:GLY156 2.3 16.5 1.0 O A:TYR177 2.3 18.6 1.0 OD2 A:ASP142 2.4 16.1 1.0 O A:HOH6006 2.5 13.8 1.0 OG1 A:THR176 2.8 17.9 1.0 CG A:ASP142 3.3 15.9 1.0 C A:GLY156 3.4 16.7 1.0 C A:TYR177 3.4 18.8 1.0 CZ A:TYR165 3.5 18.4 1.0 OD1 A:ASP142 3.7 15.1 1.0 CB A:THR176 3.7 17.8 1.0 CA A:GLY156 3.8 16.4 1.0 CB A:ASN178 4.0 19.1 1.0 CE1 A:TYR165 4.0 18.3 1.0 N A:TYR177 4.0 18.7 1.0 N A:ASN178 4.1 19.0 1.0 CA A:ASN178 4.2 19.1 1.0 CA A:TYR177 4.3 18.8 1.0 OH A:TYR189 4.3 14.9 1.0 C A:THR176 4.4 18.2 1.0 CB A:ASP142 4.5 15.8 1.0 N A:SER157 4.5 16.9 1.0 OD1 A:ASN178 4.6 21.5 1.0 O A:HIS155 4.6 16.0 1.0 CE2 A:TYR165 4.6 18.0 1.0 CG2 A:THR176 4.7 17.7 1.0 CG A:ASN178 4.7 19.6 1.0 CA A:THR176 4.7 17.9 1.0 C A:SER157 4.8 17.0 1.0 N A:LEU158 4.9 16.9 1.0 N A:ASP142 4.9 15.9 1.0 N A:GLY156 5.0 16.2 1.0 CA A:SER157 5.0 17.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain


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 the Porcine Crw-8 Rotavirus VP8* Carbohydrate- Recognising Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na6001 b:12.0 occ:1.00 O B:GLY156 2.3 14.1 1.0 OH B:TYR165 2.3 12.8 1.0 O B:TYR177 2.4 13.8 1.0 OD2 B:ASP142 2.4 13.6 1.0 O B:HOH6055 2.5 15.9 1.0 OG1 B:THR176 2.8 14.0 1.0 CG B:ASP142 3.3 14.1 1.0 C B:TYR177 3.4 13.7 1.0 C B:GLY156 3.4 14.1 1.0 CZ B:TYR165 3.5 13.3 1.0 CB B:THR176 3.6 13.3 1.0 OD1 B:ASP142 3.7 13.2 1.0 CA B:GLY156 3.9 14.2 1.0 N B:TYR177 3.9 13.4 1.0 CE1 B:TYR165 4.0 12.4 1.0 CB B:ASN178 4.0 14.7 1.0 N B:ASN178 4.2 14.0 1.0 C B:THR176 4.3 13.5 1.0 CA B:ASN178 4.3 14.3 1.0 CA B:TYR177 4.3 13.4 1.0 OH B:TYR189 4.3 16.2 1.0 CB B:ASP142 4.5 13.9 1.0 N B:SER157 4.6 13.9 1.0 CA B:THR176 4.6 13.6 1.0 OD1 B:ASN178 4.6 16.8 1.0 CE2 B:TYR165 4.7 13.2 1.0 CG2 B:THR176 4.7 13.7 1.0 CG B:ASN178 4.8 15.1 1.0 O B:HIS155 4.8 14.5 1.0 O B:THR176 4.8 14.0 1.0 C B:SER157 4.9 13.5 1.0

H.Blanchard, X.Yu, B.S.Coulson, M.Von Itzstein. Insight Into Host Cell Carbohydrate-Recognition By Human and Porcine Rotavirus From Crystal Structures of the Virion Spike Associated Carbohydrate-Binding Domain (VP8*) J.Mol.Biol. V. 367 1215 2007.
ISSN: ISSN 0022-2836
PubMed: 17306299
DOI: 10.1016/J.JMB.2007.01.028