Sodium in PDB 6h6z: Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62

The structure of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62, PDB code: 6h6z 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)	46.67 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.240, 89.640, 61.920, 90.00, 107.80, 90.00
R / Rfree (%)	17.8 / 21.7

The binding sites of Sodium atom in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62 (pdb code 6h6z). 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, PDB code: 6h6z:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:43.7 occ:1.00 O A:HOH729 2.1 42.1 1.0 O A:GLY396 2.2 40.6 1.0 O A:PHE352 2.3 34.4 1.0 O A:ASN394 2.6 35.6 1.0 C A:GLY396 3.4 40.6 1.0 C A:PHE352 3.5 33.5 1.0 C A:ASN394 3.6 35.6 1.0 CG A:ASN394 3.7 39.0 1.0 ND2 A:ASN394 3.7 40.0 1.0 O A:PRO349 3.8 38.7 1.0 CD2 A:PHE352 4.0 38.7 1.0 CB A:ASN394 4.0 35.0 1.0 OD1 A:ASN394 4.1 39.0 1.0 N A:GLY396 4.1 35.5 1.0 CB A:PHE352 4.1 34.4 1.0 C A:TYR395 4.1 35.2 1.0 O A:THR347 4.2 37.2 1.0 CA A:PHE352 4.3 33.7 1.0 CA A:GLY396 4.3 38.7 1.0 N A:SER397 4.4 43.9 1.0 CA A:SER397 4.4 44.7 1.0 O A:TYR395 4.4 33.7 1.0 CA A:ASN394 4.4 35.6 1.0 N A:TYR395 4.5 34.9 1.0 N A:VAL353 4.5 32.9 1.0 CA A:VAL353 4.5 34.6 1.0 CG A:PHE352 4.6 37.8 1.0 CB A:SER397 4.6 46.3 1.0 CA A:TYR395 4.6 32.9 1.0 N A:PHE352 4.7 36.9 1.0 C A:PRO349 4.8 39.5 1.0 O A:THR348 4.8 37.5 1.0 O A:HOH730 4.9 44.8 1.0

Sodium binding site 2 out of 2 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-62


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:58.2 occ:1.00 O B:PHE352 2.3 50.3 1.0 O B:GLY396 2.3 61.4 1.0 O B:HOH712 2.4 39.0 1.0 O B:ASN394 2.5 43.9 1.0 ND2 B:ASN394 3.4 58.2 1.0 C B:GLY396 3.5 63.5 1.0 C B:PHE352 3.5 49.1 1.0 CG B:ASN394 3.5 57.2 1.0 C B:ASN394 3.6 48.1 1.0 CB B:ASN394 3.9 53.4 1.0 O B:PRO349 3.9 51.6 1.0 OD1 B:ASN394 4.0 60.1 1.0 CD1 B:PHE352 4.0 44.5 1.0 N B:GLY396 4.1 55.9 1.0 C B:TYR395 4.2 50.1 1.0 CB B:PHE352 4.2 45.0 1.0 CG1 B:VAL353 4.3 51.2 1.0 CA B:PHE352 4.4 47.6 1.0 N B:SER397 4.4 69.4 1.0 CA B:ASN394 4.4 51.2 1.0 CA B:GLY396 4.4 58.6 1.0 CA B:SER397 4.4 73.5 1.0 O B:TYR395 4.4 49.2 1.0 N B:VAL353 4.4 48.0 1.0 O B:THR347 4.4 54.3 1.0 CA B:VAL353 4.5 49.4 1.0 N B:TYR395 4.5 49.1 1.0 CG B:PHE352 4.6 44.2 1.0 CA B:TYR395 4.7 46.8 1.0 N B:PHE352 4.7 50.4 1.0 CB B:SER397 5.0 73.3 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