Sodium in PDB 3ast: Crystal Structure of P Domain Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B

The structure of Crystal Structure of P Domain Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B, PDB code: 3ast 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)	23.92 / 1.40
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	74.966, 74.966, 107.250, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 21.2

The binding sites of Sodium atom in the Crystal Structure of P Domain Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B (pdb code 3ast). 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 Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B, PDB code: 3ast:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of P Domain Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B


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 Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:34.3 occ:1.00 O A:HOH2280 2.3 28.5 1.0 O A:PHE360 2.4 16.4 1.0 O A:GLY407 2.6 27.5 1.0 O A:ASP405 2.9 20.2 1.0 C A:PHE360 3.6 16.4 1.0 C A:GLY407 3.8 27.3 1.0 C A:ASP405 3.8 20.1 1.0 CG A:ASP405 3.9 21.8 1.0 CB A:ASP405 4.0 20.5 1.0 OD1 A:ASP405 4.2 23.4 1.0 CG1 A:VAL361 4.2 16.4 1.0 O A:VAL357 4.2 21.6 1.0 OD2 A:ASP405 4.3 24.4 1.0 N A:GLY407 4.4 23.7 1.0 C A:TYR406 4.4 22.0 1.0 CD2 A:PHE360 4.4 15.2 1.0 CB A:PHE360 4.4 16.5 1.0 CA A:PHE360 4.5 16.7 1.0 CA A:ASP405 4.5 20.1 1.0 N A:VAL361 4.5 16.1 1.0 CA A:VAL361 4.6 16.1 1.0 O A:TYR406 4.6 21.6 1.0 N A:TYR406 4.6 20.4 1.0 N A:SER408 4.6 28.7 1.0 CA A:GLY407 4.7 25.8 1.0 CA A:SER408 4.7 30.1 1.0 O A:THR355 4.7 20.1 1.0 CA A:TYR406 4.9 20.7 1.0 N A:PHE360 4.9 17.5 1.0 CG A:PHE360 4.9 15.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of P Domain Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B


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 Q389N Mutant From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:17.3 occ:1.00 O B:PHE360 2.3 12.0 1.0 O B:HOH2450 2.4 29.0 1.0 O B:HOH2265 2.4 20.7 1.0 O B:GLY407 2.4 21.6 1.0 O B:ASP405 2.5 15.9 1.0 C B:PHE360 3.5 12.4 1.0 C B:ASP405 3.6 16.0 1.0 C B:GLY407 3.6 21.7 1.0 CG B:ASP405 3.9 19.1 1.0 CB B:ASP405 3.9 17.3 1.0 N B:GLY407 4.1 18.3 1.0 C B:TYR406 4.1 17.1 1.0 OD1 B:ASP405 4.1 21.5 1.0 CD2 B:PHE360 4.2 11.5 1.0 CG1 B:VAL361 4.2 13.1 1.0 O B:HOH2476 4.3 42.7 1.0 O B:VAL357 4.3 16.2 1.0 OD2 B:ASP405 4.4 22.4 1.0 O B:TYR406 4.4 16.7 1.0 CB B:PHE360 4.4 12.5 1.0 CA B:ASP405 4.4 16.5 1.0 CA B:GLY407 4.4 20.4 1.0 N B:VAL361 4.4 12.1 1.0 CA B:PHE360 4.5 12.6 1.0 CA B:VAL361 4.5 12.2 1.0 N B:TYR406 4.5 15.9 1.0 N B:SER408 4.6 23.2 1.0 O B:THR355 4.6 15.9 1.0 CA B:TYR406 4.7 16.0 1.0 CA B:SER408 4.7 24.8 1.0 CG B:PHE360 4.8 11.5 1.0 N B:PHE360 4.9 13.1 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