Sodium in PDB 6gw1: Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca)

The structure of Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca), PDB code: 6gw1 was solved by T.Kilic, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.850, 79.670, 87.690, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19

The binding sites of Sodium atom in the Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca) (pdb code 6gw1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca), PDB code: 6gw1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:34.3 occ:1.00 O A:THR327 2.6 22.1 1.0 OG1 A:THR275 2.7 22.5 1.0 OH A:TYR416 2.7 25.4 1.0 O A:PRO328 3.0 23.8 1.0 CB A:ASP329 3.3 22.2 1.0 C A:PRO328 3.3 24.5 1.0 CA A:ASP329 3.4 23.9 1.0 CG2 A:THR275 3.4 21.8 1.0 CZ A:TYR416 3.4 26.2 1.0 N A:ASP329 3.5 22.0 1.0 CE1 A:TYR416 3.5 24.7 1.0 C A:THR327 3.5 21.3 1.0 CB A:THR275 3.6 22.1 1.0 CB A:GLN262 3.7 23.0 1.0 ND2 A:ASN263 4.0 22.5 1.0 CB A:THR327 4.1 21.7 1.0 CG2 A:THR327 4.3 23.1 1.0 N A:PRO328 4.3 20.4 1.0 CA A:PRO328 4.3 23.0 1.0 CA A:THR327 4.3 21.3 1.0 CG A:ASN263 4.5 25.0 1.0 CG A:GLN262 4.5 25.0 1.0 OD1 A:ASN263 4.5 25.4 1.0 CG A:ASP329 4.6 24.9 1.0 CE2 A:TYR416 4.6 25.8 1.0 CD1 A:TYR416 4.8 24.3 1.0 N A:THR327 4.8 23.8 1.0 C A:GLN262 4.8 22.9 1.0 CA A:GLN262 4.8 22.8 1.0 C A:ASP329 4.8 25.6 1.0 N A:ASN263 4.9 22.2 1.0 CA A:THR275 4.9 21.6 1.0

Sodium binding site 2 out of 2 in the Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gii.10 Human Norovirus Protruding Domain in Complex with Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na600 b:31.3 occ:1.00 OH B:TYR416 2.7 24.7 1.0 OG1 B:THR275 2.7 21.5 1.0 O B:THR327 2.8 21.6 1.0 O B:PRO328 3.2 23.0 1.0 CB B:ASP329 3.3 22.7 1.0 CG2 B:THR275 3.4 19.9 1.0 CA B:ASP329 3.4 21.4 1.0 CZ B:TYR416 3.4 24.0 1.0 C B:PRO328 3.4 23.2 1.0 CE2 B:TYR416 3.5 24.3 1.0 CB B:THR275 3.5 21.3 1.0 N B:ASP329 3.6 21.6 1.0 CB B:GLN262 3.6 20.7 1.0 C B:THR327 3.7 20.2 1.0 ND2 B:ASN263 4.0 22.4 1.0 CB B:THR327 4.3 20.5 1.0 CG2 B:THR327 4.4 22.2 1.0 CA B:PRO328 4.4 21.1 1.0 CG B:GLN262 4.4 22.3 1.0 N B:PRO328 4.5 19.1 1.0 CG B:ASN263 4.5 23.8 1.0 CA B:THR327 4.5 20.1 1.0 OD1 B:ASN263 4.5 21.7 1.0 CE1 B:TYR416 4.6 23.8 1.0 CG B:ASP329 4.6 25.3 1.0 CA B:GLN262 4.7 19.9 1.0 C B:GLN262 4.7 20.3 1.0 CD2 B:TYR416 4.8 21.3 1.0 N B:ASN263 4.8 20.5 1.0 C B:ASP329 4.9 21.9 1.0 N B:THR327 4.9 19.6 1.0 CA B:THR275 4.9 22.1 1.0

T.Kilic, A.Koromyslova, G.S.Hansman. Structural Basis For Human Norovirus Capsid Binding to Bile Acids. J. Virol. V. 93 2019.
ISSN: ESSN 1098-5514
PubMed: 30355683
DOI: 10.1128/JVI.01581-18