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

Protein crystallography data

The structure of Crystal Structure of P Domain From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B, PDB code: 3ass 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) 31.23 / 1.60
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 74.690, 74.690, 106.973, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 20.2

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3ass

Go back to Sodium Binding Sites List in 3ass
Sodium binding site 1 out of 2 in the Crystal Structure of P Domain 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 From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:33.9
occ:1.00
O A:HOH2335 2.3 34.6 1.0
O A:PHE360 2.3 21.9 1.0
O A:GLY407 2.5 33.4 1.0
O A:ASP405 2.7 24.6 1.0
C A:PHE360 3.6 21.9 1.0
C A:ASP405 3.7 24.6 1.0
C A:GLY407 3.7 33.3 1.0
CB A:ASP405 4.0 25.0 1.0
CG A:ASP405 4.0 26.5 1.0
CG1 A:VAL361 4.2 22.2 1.0
OD2 A:ASP405 4.2 28.0 1.0
O A:VAL357 4.2 26.3 1.0
C A:TYR406 4.3 27.0 1.0
N A:GLY407 4.3 29.0 1.0
CD2 A:PHE360 4.3 20.4 1.0
OD1 A:ASP405 4.3 28.9 1.0
CB A:PHE360 4.4 22.1 1.0
CA A:ASP405 4.4 24.4 1.0
CA A:PHE360 4.5 22.2 1.0
N A:VAL361 4.5 21.8 1.0
CA A:VAL361 4.5 21.6 1.0
O A:TYR406 4.5 26.6 1.0
N A:TYR406 4.5 24.9 1.0
CA A:SER408 4.6 36.8 1.0
N A:SER408 4.6 35.0 1.0
CA A:GLY407 4.6 31.5 1.0
O A:THR355 4.7 25.1 1.0
CA A:TYR406 4.8 25.5 1.0
CG A:PHE360 4.9 21.6 1.0
N A:PHE360 4.9 22.8 1.0

Sodium binding site 2 out of 2 in 3ass

Go back to Sodium Binding Sites List in 3ass
Sodium binding site 2 out of 2 in the Crystal Structure of P Domain 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 From Norovirus FUNABASHI258 Stain in the Complex with Lewis-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:23.2
occ:1.00
O B:PHE360 2.3 16.6 1.0
O B:HOH2314 2.4 27.2 1.0
O B:GLY407 2.4 27.1 1.0
O B:ASP405 2.5 20.7 1.0
C B:GLY407 3.5 27.3 1.0
C B:ASP405 3.5 20.5 1.0
C B:PHE360 3.6 16.8 1.0
CB B:ASP405 3.9 21.7 1.0
CG B:ASP405 3.9 24.0 1.0
N B:GLY407 4.1 23.4 1.0
OD2 B:ASP405 4.1 27.3 1.0
C B:TYR406 4.1 21.9 1.0
CG1 B:VAL361 4.2 17.0 1.0
O B:VAL357 4.2 20.9 1.0
CD2 B:PHE360 4.3 15.2 1.0
CA B:ASP405 4.3 20.8 1.0
OD1 B:ASP405 4.3 27.6 1.0
O B:TYR406 4.4 21.7 1.0
CA B:GLY407 4.4 25.8 1.0
CB B:PHE360 4.4 16.2 1.0
CA B:VAL361 4.4 16.5 1.0
N B:VAL361 4.5 16.5 1.0
N B:TYR406 4.5 20.4 1.0
N B:SER408 4.5 29.0 1.0
CA B:PHE360 4.5 16.8 1.0
CA B:SER408 4.6 30.8 1.0
CA B:TYR406 4.7 20.7 1.0
O B:THR355 4.8 21.1 1.0
CG B:PHE360 4.9 15.8 1.0
N B:PHE360 4.9 17.3 1.0
CB B:VAL361 5.0 16.7 1.0

Reference:

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
Page generated: Tue Dec 15 06:02:39 2020

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