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Sodium in PDB 5n7m: Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL)

Protein crystallography data

The structure of Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL), PDB code: 5n7m was solved by G.S.Hansman, A.D.Koromyslova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.91 / 1.73
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.070, 84.070, 165.120, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL) (pdb code 5n7m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL), PDB code: 5n7m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5n7m

Go back to Sodium Binding Sites List in 5n7m
Sodium binding site 1 out of 2 in the Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:25.3
occ:1.00
O A:GLY396 2.3 24.8 1.0
O A:PHE352 2.3 22.9 1.0
O A:HOH821 2.4 23.7 1.0
O A:ASN394 2.4 21.8 1.0
O A:HOH898 2.5 32.5 1.0
ND2 A:ASN394 3.3 31.9 1.0
CG A:ASN394 3.5 31.3 1.0
C A:GLY396 3.5 28.8 1.0
C A:ASN394 3.5 20.9 1.0
C A:PHE352 3.5 21.4 1.0
CB A:ASN394 3.9 23.3 1.0
N A:GLY396 3.9 22.3 1.0
OD1 A:ASN394 4.0 32.7 1.0
C A:TYR395 4.0 22.5 1.0
CD2 A:PHE352 4.1 21.6 1.0
O A:PRO349 4.2 26.2 1.0
CG1 A:VAL353 4.3 30.2 1.0
CA A:GLY396 4.3 26.2 1.0
CA A:ASN394 4.3 22.8 1.0
O A:TYR395 4.4 21.5 1.0
CB A:PHE352 4.4 24.5 1.0
N A:TYR395 4.4 21.2 1.0
CA A:PHE352 4.4 25.1 1.0
N A:VAL353 4.4 20.7 1.0
CA A:VAL353 4.5 18.9 1.0
N A:SER397 4.5 25.9 1.0
CA A:TYR395 4.6 19.7 1.0
CA A:SER397 4.6 35.5 1.0
C A:SER397 4.7 38.1 1.0
O A:THR347 4.7 23.0 1.0
CG A:PHE352 4.7 19.5 1.0
O A:HOH719 4.8 37.5 1.0
N A:PHE352 4.8 23.2 1.0
O A:SER397 5.0 48.6 1.0

Sodium binding site 2 out of 2 in 5n7m

Go back to Sodium Binding Sites List in 5n7m
Sodium binding site 2 out of 2 in the Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Protruding Domain of Gi.1 Norovirus in Complex with 2-Fucosyllactose (2FL) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:25.5
occ:1.00
O B:GLY396 2.3 27.9 1.0
O B:PHE352 2.3 19.0 1.0
O B:HOH818 2.4 22.8 1.0
O B:ASN394 2.4 22.6 1.0
O B:HOH894 2.5 29.0 1.0
ND2 B:ASN394 3.3 30.5 1.0
C B:ASN394 3.5 21.1 1.0
CG B:ASN394 3.5 26.7 1.0
C B:GLY396 3.5 34.3 1.0
C B:PHE352 3.6 19.9 1.0
CB B:ASN394 3.9 23.2 1.0
N B:GLY396 3.9 23.3 1.0
OD1 B:ASN394 4.0 33.7 1.0
C B:TYR395 4.0 23.1 1.0
CD2 B:PHE352 4.1 19.9 1.0
O B:PRO349 4.2 26.3 1.0
CA B:ASN394 4.3 20.6 1.0
CG1 B:VAL353 4.3 30.1 1.0
CA B:GLY396 4.3 25.2 1.0
O B:TYR395 4.3 19.8 1.0
CB B:PHE352 4.4 20.7 1.0
N B:TYR395 4.4 20.1 1.0
CA B:PHE352 4.5 22.0 1.0
N B:VAL353 4.5 20.5 1.0
CA B:VAL353 4.5 22.1 1.0
N B:SER397 4.5 33.5 1.0
CA B:TYR395 4.6 19.8 1.0
CA B:SER397 4.6 36.2 1.0
O B:THR347 4.6 23.9 1.0
CG B:PHE352 4.7 19.9 1.0
C B:SER397 4.7 44.7 1.0
O B:HOH722 4.7 38.8 1.0
N B:PHE352 4.8 24.5 1.0
O B:SER397 5.0 48.1 1.0

Reference:

A.Koromyslova, S.Tripathi, V.Morozov, H.Schroten, G.S.Hansman. Human Norovirus Inhibition By A Human Milk Oligosaccharide. Virology V. 508 81 2017.
ISSN: ISSN 1096-0341
PubMed: 28505592
DOI: 10.1016/J.VIROL.2017.04.032
Page generated: Tue Dec 15 11:19:57 2020

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