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

The structure of Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with Lewis-A, PDB code: 3asr 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)	31.25 / 1.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	74.733, 74.733, 107.039, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 21.8

The binding sites of Sodium atom in the Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with Lewis-A (pdb code 3asr). 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 Lewis-A, PDB code: 3asr:
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 Lewis-A


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 Lewis-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:35.4 occ:1.00 O A:HOH2412 2.2 43.1 1.0 O A:PHE360 2.4 29.4 1.0 O A:GLY407 2.5 38.7 1.0 O A:ASP405 2.6 31.8 1.0 C A:ASP405 3.6 31.9 1.0 C A:PHE360 3.6 29.5 1.0 C A:GLY407 3.7 38.8 1.0 CB A:ASP405 3.9 32.5 1.0 OD2 A:ASP405 3.9 35.5 1.0 CG A:ASP405 4.0 33.9 1.0 O A:VAL357 4.2 33.5 1.0 N A:GLY407 4.2 35.2 1.0 C A:TYR406 4.3 33.5 1.0 CG1 A:VAL361 4.3 30.0 1.0 CD2 A:PHE360 4.3 28.1 1.0 CA A:ASP405 4.3 31.9 1.0 CB A:PHE360 4.4 29.4 1.0 O A:TYR406 4.5 33.4 1.0 N A:TYR406 4.5 32.0 1.0 N A:VAL361 4.5 29.4 1.0 CA A:PHE360 4.5 29.7 1.0 CA A:VAL361 4.5 29.4 1.0 N A:SER408 4.6 40.3 1.0 CA A:GLY407 4.6 37.3 1.0 CA A:SER408 4.6 42.1 1.0 OD1 A:ASP405 4.7 36.5 1.0 CA A:TYR406 4.7 32.2 1.0 O A:THR355 4.8 32.4 1.0 CG A:PHE360 4.9 29.2 1.0 N A:PHE360 5.0 30.2 1.0

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


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 Lewis-A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:28.8 occ:1.00 O B:HOH2021 2.3 39.5 1.0 O B:PHE360 2.3 21.9 1.0 O B:GLY407 2.3 34.0 1.0 O B:ASP405 2.5 27.3 1.0 O B:HOH2373 2.6 39.0 1.0 C B:ASP405 3.5 27.4 1.0 C B:GLY407 3.5 34.1 1.0 C B:PHE360 3.5 22.1 1.0 CB B:ASP405 3.8 28.6 1.0 CG B:ASP405 3.8 30.5 1.0 OD2 B:ASP405 3.9 34.1 1.0 N B:GLY407 4.0 30.5 1.0 C B:TYR406 4.1 28.9 1.0 O B:HOH2329 4.1 47.1 1.0 CG1 B:VAL361 4.2 22.4 1.0 O B:VAL357 4.2 26.5 1.0 CA B:ASP405 4.3 27.7 1.0 CD2 B:PHE360 4.3 21.0 1.0 CA B:GLY407 4.4 32.8 1.0 O B:TYR406 4.4 28.6 1.0 N B:TYR406 4.4 27.4 1.0 CB B:PHE360 4.4 22.1 1.0 N B:VAL361 4.4 21.8 1.0 CA B:VAL361 4.4 21.9 1.0 OD1 B:ASP405 4.4 34.1 1.0 CA B:PHE360 4.5 22.4 1.0 N B:SER408 4.5 35.9 1.0 CA B:TYR406 4.6 27.6 1.0 CA B:SER408 4.6 37.8 1.0 N B:PHE360 4.9 23.1 1.0 CG B:PHE360 4.9 21.6 1.0 CB B:VAL361 5.0 22.1 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