Chlorine in PDB 6h6y: Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7

The structure of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7, PDB code: 6h6y was solved by T.Kilic, K.Ruoff, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.54 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.170, 140.900, 92.150, 90.00, 91.81, 90.00
R / Rfree (%)	15.5 / 17.5

The structure of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 also contains other interesting chemical elements:

Sodium

(Na)

10 atoms

The binding sites of Chlorine atom in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 (pdb code 6h6y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7, PDB code: 6h6y:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl200 b:21.0 occ:1.00 HH22 E:ARG100 2.3 20.8 1.0 H A:VAL282 2.5 15.8 1.0 HH12 E:ARG100 2.7 21.6 1.0 HA A:PRO281 3.0 15.3 1.0 O E:HOH351 3.1 19.1 1.0 HD23 E:LEU101 3.1 26.8 1.0 NH2 E:ARG100 3.1 17.3 1.0 O A:HOH805 3.2 30.7 1.0 HG12 A:VAL282 3.2 19.8 1.0 N A:VAL282 3.3 13.1 1.0 HB2 B:SER240 3.3 20.9 1.0 NH1 E:ARG100 3.4 18.0 1.0 CZ E:ARG100 3.7 16.7 1.0 HD22 E:LEU101 3.7 26.8 1.0 CA A:PRO281 3.7 12.8 1.0 HB2 A:PRO281 3.7 16.6 1.0 HH21 E:ARG100 3.7 20.8 1.0 HG23 A:ILE318 3.8 18.6 1.0 HB A:VAL282 3.8 17.3 1.0 CD2 E:LEU101 3.8 22.3 1.0 HB3 A:PRO281 3.8 16.6 1.0 CB A:PRO281 4.0 13.8 1.0 CG1 A:VAL282 4.0 16.5 1.0 C A:PRO281 4.0 13.5 1.0 HH11 E:ARG100 4.1 21.6 1.0 HG11 A:VAL282 4.1 19.8 1.0 HD21 E:LEU101 4.2 26.8 1.0 CB B:SER240 4.2 17.4 1.0 CB A:VAL282 4.2 14.4 1.0 HD12 A:LEU276 4.3 22.7 1.0 H A:SER283 4.3 16.4 1.0 HD11 A:ILE318 4.4 18.8 1.0 CA A:VAL282 4.4 14.3 1.0 HD11 A:LEU276 4.4 22.7 1.0 HB3 B:SER240 4.4 20.9 1.0 HD13 A:LEU276 4.4 22.7 1.0 HA B:SER240 4.5 19.4 1.0 CD1 A:LEU276 4.6 18.9 1.0 CG2 A:ILE318 4.6 15.5 1.0 ND1 A:HIS286 4.7 20.4 0.4 HG22 A:ILE318 4.8 18.6 1.0 O B:SER240 4.8 19.0 1.0 HG13 A:VAL282 4.8 19.8 1.0 HG21 A:ILE318 4.8 18.6 1.0 CA B:SER240 4.9 16.2 1.0 HD13 E:LEU101 5.0 27.5 1.0 O A:THR280 5.0 14.2 1.0 NE E:ARG100 5.0 17.4 1.0 O E:HOH352 5.0 35.8 1.0 N A:SER283 5.0 13.6 1.0 CG E:LEU101 5.0 20.2 1.0

Chlorine binding site 2 out of 4 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl200 b:22.2 occ:1.00 HH22 F:ARG100 2.3 22.9 1.0 H B:VAL282 2.5 17.8 1.0 HH12 F:ARG100 2.7 22.5 1.0 HA B:PRO281 3.0 17.2 1.0 O B:HOH733 3.0 20.4 1.0 NH2 F:ARG100 3.1 19.1 1.0 HD22 F:LEU101 3.2 26.0 1.0 N B:VAL282 3.3 14.8 1.0 O B:HOH819 3.3 30.6 1.0 HB2 A:SER240 3.3 20.3 1.0 HG11 B:VAL282 3.4 19.3 1.0 NH1 F:ARG100 3.4 18.9 1.0 CA B:PRO281 3.7 14.3 1.0 CZ F:ARG100 3.7 18.9 1.0 HB2 B:PRO281 3.7 18.9 1.0 HG23 B:ILE318 3.8 19.9 1.0 HH21 F:ARG100 3.8 22.9 1.0 HB B:VAL282 3.8 18.0 1.0 HD21 F:LEU101 3.8 26.0 1.0 HB3 B:PRO281 3.8 18.9 1.0 CD2 F:LEU101 3.9 21.6 1.0 CB B:PRO281 3.9 15.7 1.0 C B:PRO281 4.0 14.7 1.0 CG1 B:VAL282 4.0 16.1 1.0 HG13 B:VAL282 4.0 19.3 1.0 HH11 F:ARG100 4.1 22.5 1.0 CB B:VAL282 4.2 15.0 1.0 CB A:SER240 4.3 16.9 1.0 H B:SER283 4.3 17.6 1.0 CA B:VAL282 4.3 13.6 1.0 HD12 B:LEU276 4.3 20.6 1.0 HD11 B:LEU276 4.4 20.6 1.0 HD23 F:LEU101 4.4 26.0 1.0 HD13 B:LEU276 4.4 20.6 1.0 HB3 A:SER240 4.4 20.3 1.0 HD12 B:ILE318 4.4 24.0 1.0 HA A:SER240 4.5 18.6 1.0 CD1 B:LEU276 4.6 17.2 1.0 CG2 B:ILE318 4.6 16.5 1.0 HG22 B:ILE318 4.8 19.9 1.0 HG21 B:ILE318 4.8 19.9 1.0 O A:SER240 4.8 17.6 1.0 HG12 B:VAL282 4.9 19.3 1.0 CA A:SER240 4.9 15.6 1.0 O B:THR280 4.9 15.8 1.0 N B:SER283 5.0 14.6 1.0 N B:PRO281 5.0 14.1 1.0 NE F:ARG100 5.0 18.9 1.0

Chlorine binding site 3 out of 4 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl200 b:22.8 occ:1.00 HH22 G:ARG100 2.4 21.8 1.0 H C:VAL282 2.4 17.0 1.0 HH12 G:ARG100 2.7 24.0 1.0 HA C:PRO281 3.0 17.6 1.0 O C:HOH729 3.0 20.4 1.0 NH2 G:ARG100 3.1 18.1 1.0 HD23 G:LEU101 3.2 26.4 1.0 N C:VAL282 3.3 14.1 1.0 HG11 C:VAL282 3.3 22.0 1.0 NH1 G:ARG100 3.4 20.0 1.0 HB2 D:SER240 3.4 23.5 1.0 CA C:PRO281 3.7 14.7 1.0 HB2 C:PRO281 3.7 16.7 1.0 CZ G:ARG100 3.7 19.8 1.0 HG21 C:ILE318 3.7 17.7 1.0 HB C:VAL282 3.8 20.0 1.0 HH21 G:ARG100 3.8 21.8 1.0 HB3 C:PRO281 3.8 16.7 1.0 HG13 C:VAL282 3.9 22.0 1.0 CB C:PRO281 3.9 13.9 1.0 CG1 C:VAL282 3.9 18.3 1.0 C C:PRO281 4.0 14.4 1.0 CD2 G:LEU101 4.1 22.0 1.0 HH11 G:ARG100 4.1 24.0 1.0 HD22 G:LEU101 4.1 26.4 1.0 CB C:VAL282 4.2 16.6 1.0 CB D:SER240 4.3 19.6 1.0 CA C:VAL282 4.3 13.7 1.0 H C:SER283 4.3 18.4 1.0 HD21 G:LEU101 4.4 26.4 1.0 HD13 C:LEU276 4.4 19.6 1.0 HD12 C:LEU276 4.4 19.6 1.0 HD13 C:ILE318 4.4 19.6 1.0 HB3 D:SER240 4.5 23.5 1.0 HA D:SER240 4.5 21.8 1.0 HD11 C:LEU276 4.5 19.6 1.0 CG2 C:ILE318 4.6 14.7 1.0 CD1 C:LEU276 4.7 16.3 1.0 HG23 C:ILE318 4.7 17.7 1.0 HG22 C:ILE318 4.8 17.7 1.0 HG12 C:VAL282 4.8 22.0 1.0 O D:SER240 4.8 17.7 1.0 O C:THR280 4.9 14.3 1.0 CA D:SER240 5.0 18.2 1.0 N C:PRO281 5.0 13.6 1.0 N C:SER283 5.0 15.3 1.0

Chlorine binding site 4 out of 4 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl200 b:21.6 occ:1.00 HH22 H:ARG100 2.3 28.4 1.0 H D:VAL282 2.5 16.9 1.0 HH12 H:ARG100 2.6 26.6 1.0 HA D:PRO281 3.0 16.8 1.0 O D:HOH735 3.1 21.3 1.0 NH2 H:ARG100 3.1 23.7 1.0 HD22 H:LEU101 3.1 29.0 1.0 N D:VAL282 3.3 14.1 1.0 HB2 C:SER240 3.3 22.2 1.0 NH1 H:ARG100 3.3 22.2 1.0 HG11 D:VAL282 3.4 21.8 1.0 CZ H:ARG100 3.7 22.6 1.0 CA D:PRO281 3.7 14.0 1.0 HB D:VAL282 3.7 18.2 1.0 HH21 H:ARG100 3.8 28.4 1.0 HB2 D:PRO281 3.8 19.7 1.0 HG23 D:ILE318 3.8 17.8 1.0 HG13 D:VAL282 3.8 21.8 1.0 HB3 D:PRO281 3.9 19.7 1.0 CD2 H:LEU101 4.0 24.1 1.0 CG1 D:VAL282 4.0 18.1 1.0 HD1 D:HIS286 4.0 24.5 0.5 CB D:PRO281 4.0 16.4 1.0 HD21 H:LEU101 4.0 29.0 1.0 C D:PRO281 4.0 13.1 1.0 HH11 H:ARG100 4.1 26.6 1.0 CB D:VAL282 4.2 15.1 1.0 CB C:SER240 4.2 18.5 1.0 HD13 D:LEU276 4.2 24.1 1.0 HD12 D:LEU276 4.3 24.1 1.0 CA D:VAL282 4.3 14.4 1.0 H D:SER283 4.4 17.6 1.0 HD11 D:LEU276 4.4 24.1 1.0 HD23 H:LEU101 4.4 29.0 1.0 HB3 C:SER240 4.4 22.2 1.0 HD11 D:ILE318 4.4 20.4 1.0 HA C:SER240 4.5 19.7 1.0 CD1 D:LEU276 4.5 20.1 1.0 CG2 D:ILE318 4.6 14.8 1.0 ND1 D:HIS286 4.7 20.4 0.5 HG21 D:ILE318 4.7 17.8 1.0 O C:SER240 4.9 16.9 1.0 HG12 D:VAL282 4.9 21.8 1.0 HG22 D:ILE318 4.9 17.8 1.0 CA C:SER240 4.9 16.4 1.0 O D:THR280 4.9 15.7 1.0 NE H:ARG100 5.0 22.0 1.0 HG H:LEU101 5.0 32.7 1.0 HD11 H:LEU101 5.0 33.6 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