Sodium in PDB 3sis: Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3_GC

The structure of Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3_GC, PDB code: 3sis 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)	39.12 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.310, 56.770, 110.700, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.8

The binding sites of Sodium atom in the Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3_GC (pdb code 3sis). 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_GC, PDB code: 3sis:
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_GC


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_GC within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3000 b:22.3 occ:1.00 O A:GLY156 2.3 19.6 1.0 O A:TYR177 2.3 19.7 1.0 OH A:TYR165 2.4 22.2 1.0 OG1 A:THR176 2.6 19.8 1.0 OD2 A:ASP142 2.7 19.0 1.0 O A:HOH234 3.3 23.8 1.0 C A:GLY156 3.3 19.3 1.0 C A:TYR177 3.4 20.1 1.0 CG A:ASP142 3.5 19.6 1.0 CZ A:TYR165 3.6 21.4 1.0 CB A:THR176 3.6 20.6 1.0 CA A:GLY156 3.8 19.4 1.0 CB A:ASN178 3.8 22.6 1.0 OD1 A:ASP142 3.8 18.7 1.0 CE1 A:TYR165 3.9 21.2 1.0 N A:ASN178 4.1 20.9 1.0 N A:TYR177 4.1 19.9 1.0 CA A:ASN178 4.1 21.9 1.0 C A:THR176 4.3 20.4 1.0 CA A:TYR177 4.3 20.2 1.0 OH A:TYR189 4.4 18.3 1.0 OD1 A:ASN178 4.4 26.8 1.0 N A:PRO157 4.5 19.5 1.0 CG A:ASN178 4.5 24.5 1.0 CA A:THR176 4.6 20.2 1.0 CG2 A:THR176 4.6 19.5 1.0 C A:PRO157 4.6 19.8 1.0 CB A:ASP142 4.7 19.5 1.0 O A:HIS155 4.7 19.7 1.0 O A:THR176 4.7 20.9 1.0 CE2 A:TYR165 4.8 20.6 1.0 CA A:PRO157 4.8 19.5 1.0 N A:LEU158 4.8 20.2 1.0 CB A:LEU158 4.8 20.6 1.0 O A:PRO157 4.9 19.5 1.0 N A:GLY156 4.9 19.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Porcine Crw-8 Rotavirus VP8* in Complex with Aceramido-GM3_GC


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_GC within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3001 b:19.2 occ:1.00 O B:TYR177 2.3 19.8 1.0 O B:GLY156 2.3 19.7 1.0 OH B:TYR165 2.3 18.3 1.0 OD1 B:ASN178 2.4 16.8 0.5 OD2 B:ASP142 2.5 17.5 1.0 OG1 B:THR176 2.7 20.9 1.0 C B:TYR177 3.3 20.3 1.0 C B:GLY156 3.3 20.1 1.0 CG B:ASP142 3.4 19.4 1.0 O B:HOH55 3.5 27.9 1.0 CZ B:TYR165 3.5 19.4 1.0 CG B:ASN178 3.6 18.8 0.5 CB B:THR176 3.7 21.0 1.0 CA B:GLY156 3.8 20.2 1.0 OD1 B:ASP142 3.8 16.3 1.0 N B:TYR177 3.9 21.4 1.0 CE1 B:TYR165 3.9 19.2 1.0 CB B:ASN178 3.9 20.4 0.5 N B:ASN178 4.0 20.0 1.0 CA B:ASN178 4.0 20.4 0.5 CA B:ASN178 4.1 20.0 0.5 CA B:TYR177 4.2 20.7 1.0 CB B:ASN178 4.4 19.6 0.5 C B:THR176 4.5 21.3 1.0 OH B:TYR189 4.5 17.0 1.0 N B:PRO157 4.5 19.6 1.0 ND2 B:ASN178 4.5 18.6 0.5 CB B:ASP142 4.6 20.5 1.0 C B:PRO157 4.7 19.7 1.0 CE2 B:TYR165 4.7 18.7 1.0 CA B:THR176 4.7 20.9 1.0 CG2 B:THR176 4.7 20.1 1.0 O B:HIS155 4.8 21.1 1.0 N B:LEU158 4.8 19.5 1.0 CB B:LEU158 4.9 19.4 1.0 CG B:ASN178 4.9 21.2 0.5 CA B:PRO157 4.9 19.6 1.0 OD1 B:ASN178 4.9 22.4 0.5 O B:PRO157 4.9 19.6 1.0 N B:GLY156 4.9 20.4 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