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

The structure of Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with A-Antigen, PDB code: 3asp 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)	35.23 / 1.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	74.624, 74.624, 106.996, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.1

The binding sites of Sodium atom in the Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with A-Antigen (pdb code 3asp). 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 A-Antigen, PDB code: 3asp:
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 A-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 A-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:33.9 occ:1.00 O A:HOH2372 2.3 28.7 1.0 O A:GLY407 2.4 31.3 1.0 O A:PHE360 2.4 18.5 1.0 O A:ASP405 2.8 21.5 1.0 C A:GLY407 3.6 31.1 1.0 C A:PHE360 3.6 18.6 1.0 C A:ASP405 3.7 21.6 1.0 CG A:ASP405 3.9 23.9 1.0 CB A:ASP405 3.9 22.2 1.0 OD2 A:ASP405 4.0 25.8 1.0 N A:GLY407 4.1 26.1 1.0 CG1 A:VAL361 4.2 18.5 1.0 C A:TYR406 4.3 23.9 1.0 O A:VAL357 4.3 23.6 1.0 O A:HOH2127 4.4 38.7 1.0 OD1 A:ASP405 4.4 27.1 1.0 CD2 A:PHE360 4.4 17.1 1.0 CA A:GLY407 4.4 29.0 1.0 CA A:ASP405 4.4 21.5 1.0 CB A:PHE360 4.5 18.7 1.0 N A:TYR406 4.5 21.9 1.0 N A:VAL361 4.5 18.2 1.0 CA A:PHE360 4.5 19.0 1.0 O A:TYR406 4.6 23.3 1.0 CA A:VAL361 4.6 18.0 1.0 N A:SER408 4.6 32.9 1.0 CA A:SER408 4.7 34.8 1.0 CA A:TYR406 4.7 22.4 1.0 O A:THR355 4.8 22.3 1.0 N A:PHE360 5.0 19.5 1.0 CG A:PHE360 5.0 18.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with A-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 A-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:24.3 occ:1.00 O B:PHE360 2.3 14.7 1.0 O B:HOH2392 2.4 29.2 1.0 O B:GLY407 2.4 28.7 1.0 O B:ASP405 2.6 20.4 1.0 C B:PHE360 3.5 15.2 1.0 C B:ASP405 3.6 20.7 1.0 C B:GLY407 3.6 28.7 1.0 CG B:ASP405 3.9 23.7 1.0 CB B:ASP405 3.9 21.8 1.0 OD2 B:ASP405 4.1 25.9 1.0 N B:GLY407 4.1 24.3 1.0 CG1 B:VAL361 4.1 15.5 1.0 C B:TYR406 4.2 22.5 1.0 O B:VAL357 4.3 19.0 1.0 OD1 B:ASP405 4.3 27.6 1.0 CD2 B:PHE360 4.4 13.6 1.0 CA B:ASP405 4.4 21.0 1.0 O B:TYR406 4.4 22.0 1.0 CB B:PHE360 4.4 14.8 1.0 N B:VAL361 4.4 15.0 1.0 CA B:VAL361 4.4 14.9 1.0 N B:TYR406 4.5 20.8 1.0 CA B:PHE360 4.5 15.1 1.0 CA B:GLY407 4.5 27.0 1.0 N B:SER408 4.6 30.5 1.0 CA B:TYR406 4.7 21.1 1.0 CA B:SER408 4.7 32.4 1.0 O B:THR355 4.8 19.2 1.0 N B:PHE360 4.9 15.5 1.0 CG B:PHE360 4.9 14.4 1.0 CB B:VAL361 5.0 15.3 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