Sodium in PDB 3sit: Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3

The structure of Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3, PDB code: 3sit was solved by H.Blanchard, X.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.35 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.777, 57.357, 113.129, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.3

The binding sites of Sodium atom in the Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3 (pdb code 3sit). 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 Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3, PDB code: 3sit:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3


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 Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3000 b:10.7 occ:1.00 O A:GLY156 2.3 9.7 1.0 O A:TYR177 2.3 11.6 1.0 OH A:TYR165 2.4 9.4 1.0 O A:HOH235 2.5 13.8 1.0 OD2 A:ASP142 2.5 8.6 1.0 OG1 A:THR176 2.8 12.1 1.0 C A:GLY156 3.4 9.7 1.0 C A:TYR177 3.4 11.9 1.0 CG A:ASP142 3.4 9.4 1.0 CZ A:TYR165 3.6 9.4 1.0 CB A:THR176 3.8 12.1 1.0 OD1 A:ASP142 3.8 9.1 1.0 CA A:GLY156 3.8 9.6 1.0 CB A:ASN178 4.0 12.0 1.0 CE1 A:TYR165 4.0 9.6 1.0 N A:TYR177 4.0 12.1 1.0 N A:ASN178 4.1 11.7 1.0 CA A:ASN178 4.2 11.9 1.0 CA A:TYR177 4.3 12.0 1.0 OH A:TYR189 4.3 10.1 1.0 C A:THR176 4.3 12.4 1.0 N A:PRO157 4.5 9.4 1.0 O A:HIS155 4.6 9.7 1.0 CB A:ASP142 4.6 9.5 1.0 OD1 A:ASN178 4.7 12.0 1.0 CG A:ASN178 4.7 12.7 1.0 CE2 A:TYR165 4.7 9.4 1.0 CA A:THR176 4.7 12.2 1.0 C A:PRO157 4.7 9.6 1.0 O A:THR176 4.8 13.0 1.0 CA A:PRO157 4.9 9.6 1.0 CG2 A:THR176 4.9 12.3 1.0 N A:LEU158 4.9 9.7 1.0 N A:GLY156 4.9 9.4 1.0 N A:ASP142 5.0 9.5 1.0 O A:PRO157 5.0 9.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3


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 Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3001 b:9.7 occ:1.00 O B:GLY156 2.2 10.3 1.0 OH B:TYR165 2.3 9.0 1.0 O B:TYR177 2.4 10.1 1.0 OD2 B:ASP142 2.5 9.2 1.0 O B:HOH241 2.6 16.9 1.0 OG1 B:THR176 2.9 10.2 1.0 C B:GLY156 3.3 10.2 1.0 CG B:ASP142 3.4 9.0 1.0 C B:TYR177 3.4 10.3 1.0 CZ B:TYR165 3.5 9.1 1.0 OD1 B:ASP142 3.7 9.1 1.0 CA B:GLY156 3.8 10.5 1.0 CB B:THR176 3.8 9.9 1.0 CE1 B:TYR165 3.9 8.8 1.0 N B:TYR177 4.0 10.2 1.0 CB B:ASN178 4.0 10.8 1.0 N B:ASN178 4.2 10.2 1.0 CA B:ASN178 4.2 10.7 1.0 CA B:TYR177 4.3 10.2 1.0 OH B:TYR189 4.4 11.0 1.0 C B:THR176 4.5 10.3 1.0 N B:PRO157 4.5 10.0 1.0 CB B:ASP142 4.5 9.3 1.0 O B:HIS155 4.6 10.9 1.0 OD1 B:ASN178 4.6 13.8 1.0 CE2 B:TYR165 4.7 9.1 1.0 C B:PRO157 4.7 9.3 1.0 CG B:ASN178 4.8 12.5 1.0 CG2 B:THR176 4.8 10.3 1.0 N B:LEU158 4.8 8.9 1.0 CA B:THR176 4.8 10.1 1.0 CA B:PRO157 4.8 9.6 1.0 N B:ASP142 4.9 9.2 1.0 N B:GLY156 4.9 10.7 1.0 CB B:LEU158 4.9 8.9 1.0 O B:PRO157 5.0 8.9 1.0

X.Yu, B.S.Coulson, F.E.Fleming, J.C.Dyason, M.Von Itzstein, H.Blanchard. Novel Structural Insights Into Rotavirus Recognition of Ganglioside Glycan Receptors. J.Mol.Biol. V. 413 929 2011.
ISSN: ISSN 0022-2836
PubMed: 21945555
DOI: 10.1016/J.JMB.2011.09.005