Sodium in PDB 3asq: Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen

The structure of Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen, PDB code: 3asq was solved by T.Kubota, A.Kumagai, H.Itoh, S.Furukawa, H.Narimatsu, T.Wakita, K.Ishii, N.Takeda, Y.Someya, H.Shirato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.26 / 1.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	74.690, 74.690, 107.106, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 19.4

The binding sites of Sodium atom in the Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen (pdb code 3asq). 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 P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen, PDB code: 3asq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen


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 P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:32.7 occ:1.00 O A:HOH2347 2.3 28.2 1.0 O A:PHE360 2.4 17.6 1.0 O A:GLY407 2.5 31.3 1.0 O A:ASP405 2.8 21.4 1.0 C A:PHE360 3.6 17.7 1.0 C A:GLY407 3.7 31.1 1.0 C A:ASP405 3.7 21.4 1.0 CG A:ASP405 3.9 23.5 1.0 CB A:ASP405 4.0 21.9 1.0 OD2 A:ASP405 4.1 25.4 1.0 CG1 A:VAL361 4.2 17.9 1.0 OD1 A:ASP405 4.2 26.7 1.0 N A:GLY407 4.2 26.4 1.0 C A:TYR406 4.3 24.2 1.0 O A:VAL357 4.3 22.7 1.0 CD2 A:PHE360 4.4 16.1 1.0 CB A:PHE360 4.4 17.8 1.0 CA A:ASP405 4.5 21.3 1.0 O A:TYR406 4.5 23.7 1.0 CA A:PHE360 4.5 17.9 1.0 N A:VAL361 4.5 17.7 1.0 CA A:VAL361 4.5 17.5 1.0 N A:TYR406 4.5 22.0 1.0 CA A:GLY407 4.6 29.1 1.0 N A:SER408 4.6 32.8 1.0 O A:THR355 4.6 21.0 1.0 CA A:SER408 4.7 34.6 1.0 CA A:TYR406 4.8 22.6 1.0 CG A:PHE360 4.9 17.1 1.0 N A:PHE360 4.9 18.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen


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 P Domain From Norovirus FUNABASHI258 Stain in the Complex with H-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:21.1 occ:1.00 O B:PHE360 2.3 13.3 1.0 O B:HOH2410 2.4 31.7 1.0 O B:GLY407 2.4 25.0 1.0 O B:HOH2021 2.4 23.2 1.0 O B:ASP405 2.5 17.8 1.0 C B:PHE360 3.5 13.7 1.0 C B:ASP405 3.5 17.9 1.0 C B:GLY407 3.6 25.2 1.0 CG B:ASP405 3.8 21.4 1.0 CB B:ASP405 3.9 19.2 1.0 N B:GLY407 4.1 21.2 1.0 OD2 B:ASP405 4.1 24.1 1.0 C B:TYR406 4.1 19.7 1.0 CD2 B:PHE360 4.2 12.2 1.0 OD1 B:ASP405 4.2 25.0 1.0 CG1 B:VAL361 4.2 14.1 1.0 O B:VAL357 4.3 17.4 1.0 O B:TYR406 4.3 19.3 1.0 CA B:ASP405 4.3 18.4 1.0 O B:HOH2411 4.3 39.2 1.0 CB B:PHE360 4.4 13.4 1.0 CA B:GLY407 4.4 23.7 1.0 N B:VAL361 4.4 13.4 1.0 CA B:VAL361 4.4 13.7 1.0 N B:TYR406 4.4 18.0 1.0 CA B:PHE360 4.4 13.7 1.0 N B:SER408 4.5 27.0 1.0 CA B:TYR406 4.6 18.2 1.0 CA B:SER408 4.7 28.9 1.0 O B:THR355 4.7 17.6 1.0 CG B:PHE360 4.8 12.9 1.0 N B:PHE360 4.9 14.2 1.0 CB B:VAL361 5.0 13.9 1.0

T.Kubota, A.Kumagai, H.Ito, S.Furukawa, Y.Someya, N.Takeda, K.Ishii, T.Wakita, H.Narimatsu, H.Shirato. Structural Basis For the Recognition of Lewis Antigens By Genogroup I Norovirus J.Virol. V. 86 11138 2012.
ISSN: ISSN 0022-538X
PubMed: 22855491
DOI: 10.1128/JVI.00278-12