Atomistry » Sodium » PDB 5mse-5nb4 » 5n7m
Atomistry »
  Sodium »
    PDB 5mse-5nb4 »
      5n7m »

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

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy