Sodium in PDB 3tay: Crystal Structure of Porcine Rotavirus Crw-8 VP8* in Complex with N- Glycolylneuraminic Acid

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

Resolution Low / High (Å)	40.03 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.982, 59.646, 111.964, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.5

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

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


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 Rotavirus Crw-8 VP8* in Complex with N- Glycolylneuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:12.8 occ:1.00 O A:GLY156 2.2 10.3 1.0 O A:TYR177 2.3 11.6 1.0 OH A:TYR165 2.4 10.4 1.0 OD2 A:ASP142 2.5 8.5 1.0 OG1 A:THR176 2.8 12.4 1.0 O A:HOH342 2.9 20.9 1.0 C A:TYR177 3.3 12.0 1.0 C A:GLY156 3.3 9.9 1.0 CG A:ASP142 3.4 9.2 1.0 CZ A:TYR165 3.6 10.4 1.0 OD1 A:ASP142 3.7 8.7 1.0 CB A:THR176 3.8 12.5 1.0 CA A:GLY156 3.9 9.8 1.0 CB A:ASN178 3.9 12.8 1.0 CE1 A:TYR165 4.0 10.8 1.0 N A:TYR177 4.0 12.0 1.0 N A:ASN178 4.1 12.1 1.0 CA A:ASN178 4.1 12.5 1.0 CA A:TYR177 4.3 11.8 1.0 OH A:TYR189 4.4 10.8 1.0 C A:THR176 4.5 12.4 1.0 N A:SER157 4.5 10.0 1.0 CB A:ASP142 4.6 8.7 1.0 OD1 A:ASN178 4.6 15.9 1.0 O A:HIS155 4.7 9.4 1.0 C A:SER157 4.7 9.4 1.0 CE2 A:TYR165 4.7 10.2 1.0 CG A:ASN178 4.7 14.2 1.0 CG2 A:THR176 4.8 12.6 1.0 CA A:THR176 4.8 12.5 1.0 N A:LEU158 4.8 8.9 1.0 CA A:SER157 4.9 9.9 1.0 O A:SER157 5.0 9.2 1.0 N A:ASP142 5.0 8.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Porcine Rotavirus Crw-8 VP8* in Complex with N- Glycolylneuraminic Acid


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 Rotavirus Crw-8 VP8* in Complex with N- Glycolylneuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:10.6 occ:1.00 O B:GLY156 2.2 8.6 1.0 OD1 B:ASN178 2.3 7.1 0.5 OH B:TYR165 2.3 6.8 1.0 O B:TYR177 2.4 7.2 1.0 OD2 B:ASP142 2.6 7.3 1.0 OG1 B:THR176 2.6 7.5 1.0 O B:HOH363 2.7 12.9 0.5 C B:TYR177 3.3 7.0 1.0 C B:GLY156 3.4 8.5 1.0 CG B:ASP142 3.5 8.2 1.0 CG B:ASN178 3.5 7.7 0.5 CZ B:TYR165 3.5 7.0 1.0 CB B:THR176 3.6 7.3 1.0 OD1 B:ASP142 3.8 8.6 1.0 CE1 B:TYR165 3.9 7.1 1.0 CA B:GLY156 3.9 8.8 1.0 CB B:ASN178 3.9 7.8 0.5 N B:TYR177 4.0 6.9 1.0 N B:ASN178 4.1 7.4 1.0 CA B:ASN178 4.1 7.6 0.5 CA B:ASN178 4.1 7.5 0.5 CB B:ASN178 4.2 7.6 0.5 CA B:TYR177 4.3 6.9 1.0 C B:THR176 4.3 7.2 1.0 OH B:TYR189 4.4 8.4 1.0 N B:SER157 4.5 7.7 1.0 ND2 B:ASN178 4.5 8.3 0.5 CA B:THR176 4.6 7.1 1.0 CG2 B:THR176 4.6 7.9 1.0 CE2 B:TYR165 4.7 6.7 1.0 CB B:ASP142 4.7 7.9 1.0 C B:SER157 4.7 7.1 1.0 CG B:ASN178 4.8 8.4 0.5 O B:HIS155 4.8 9.9 1.0 CA B:SER157 4.8 7.5 1.0 N B:LEU158 4.9 6.8 1.0 O B:SER157 4.9 6.6 1.0 O B:THR176 4.9 7.4 1.0 CB B:LEU158 5.0 6.6 1.0

X.Yu, V.T.Dang, F.E.Fleming, M.Von Itzstein, B.S.Coulson, H.Blanchard. Structural Basis of Rotavirus Strain Preference Toward N-Acetyl- or N-Glycolylneuraminic Acid-Containing Receptors. J.Virol. V. 86 13456 2012.
ISSN: ISSN 0022-538X
PubMed: 23035213
DOI: 10.1128/JVI.06975-11