Sodium in PDB 6h70: Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 2- Fucosyllactose (2FL)

The structure of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 2- Fucosyllactose (2FL), PDB code: 6h70 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)	46.76 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.170, 89.210, 62.150, 90.00, 106.92, 90.00
R / Rfree (%)	16.2 / 19.1

The binding sites of Sodium atom in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 2- Fucosyllactose (2FL) (pdb code 6h70). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 2- Fucosyllactose (2FL), PDB code: 6h70:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 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 Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 2- Fucosyllactose (2FL) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:29.4 occ:1.00 O A:GLY396 2.1 31.4 1.0 O A:HOH768 2.2 23.3 1.0 O A:PHE352 2.3 23.4 1.0 O A:ASN394 2.5 22.1 1.0 C A:GLY396 3.3 26.0 1.0 C A:ASN394 3.5 22.5 1.0 C A:PHE352 3.5 23.5 1.0 ND2 A:ASN394 3.5 32.8 1.0 CG A:ASN394 3.6 31.2 1.0 N A:GLY396 3.9 20.9 1.0 CD2 A:PHE352 3.9 18.2 1.0 C A:TYR395 3.9 21.7 1.0 CB A:ASN394 3.9 25.0 1.0 OD1 A:ASN394 4.0 31.4 1.0 O A:PRO349 4.0 23.9 1.0 CA A:GLY396 4.2 22.8 1.0 CB A:PHE352 4.2 22.2 1.0 O A:TYR395 4.3 21.2 1.0 O A:THR347 4.3 23.4 1.0 CA A:ASN394 4.3 21.6 1.0 N A:TYR395 4.3 23.9 1.0 N A:SER397 4.3 26.4 1.0 CA A:PHE352 4.4 19.8 1.0 CA A:TYR395 4.4 20.9 1.0 CA A:SER397 4.4 27.5 1.0 N A:VAL353 4.4 20.1 1.0 CA A:VAL353 4.4 23.5 1.0 CG A:PHE352 4.5 20.1 1.0 CB A:SER397 4.6 33.4 1.0 N A:PHE352 4.8 20.6 1.0 CD A:PRO354 4.9 20.0 1.0 CE2 A:PHE352 4.9 19.7 1.0 CB A:VAL353 5.0 28.1 1.0

Sodium binding site 2 out of 2 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 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 Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 and 2- Fucosyllactose (2FL) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na600 b:29.4 occ:1.00 O B:GLY396 2.2 43.7 1.0 O B:HOH801 2.3 26.9 1.0 O B:PHE352 2.3 24.5 1.0 O B:ASN394 2.5 29.4 1.0 ND2 B:ASN394 3.2 37.8 1.0 C B:GLY396 3.4 40.7 1.0 CG B:ASN394 3.4 34.4 1.0 C B:ASN394 3.5 27.1 1.0 C B:PHE352 3.5 21.3 1.0 CB B:ASN394 3.8 26.9 1.0 OD1 B:ASN394 3.9 34.4 1.0 N B:GLY396 4.0 29.8 1.0 C B:TYR395 4.0 25.8 1.0 CD1 B:PHE352 4.1 21.5 1.0 O B:PRO349 4.1 25.4 1.0 O B:TYR395 4.2 25.0 1.0 CA B:GLY396 4.3 33.9 1.0 N B:SER397 4.3 44.5 1.0 CA B:ASN394 4.3 26.6 1.0 CB B:PHE352 4.3 22.3 1.0 CG1 B:VAL353 4.3 28.8 1.0 CA B:SER397 4.4 49.7 1.0 N B:TYR395 4.4 24.7 1.0 CA B:VAL353 4.4 22.4 1.0 CA B:PHE352 4.5 21.1 1.0 N B:VAL353 4.5 22.3 1.0 CA B:TYR395 4.5 22.8 1.0 O B:THR347 4.6 26.5 1.0 CG B:PHE352 4.7 23.2 1.0 N B:PHE352 4.9 23.9 1.0

K.Ruoff, T.Kilic, J.Devant, A.Koromyslova, A.Ringel, A.Hempelmann, C.Geiss, J.Graf, M.Haas, I.Roggenbach, G.Hansman. Structural Basis of Nanobodies Targeting the Prototype Norovirus. J. Virol. V. 93 2019.
ISSN: ESSN 1098-5514
PubMed: 30602609
DOI: 10.1128/JVI.02005-18