Chlorine in PDB 7vs8: Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.

The structure of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen., PDB code: 7vs8 was solved by K.Murayama, M.Kato-Murayama, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.19 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.749, 76.464, 103.281, 90, 124.2, 90
R / Rfree (%)	16.5 / 19.6

The structure of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. (pdb code 7vs8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen., PDB code: 7vs8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:56.8 occ:1.00 N A:GLN233 3.1 35.0 1.0 O A:THR231 3.7 51.4 1.0 CA A:LYS232 3.8 43.4 1.0 CB A:GLN233 3.9 37.6 1.0 CG A:GLN233 3.9 36.5 1.0 C A:LYS232 3.9 37.7 1.0 CA A:GLN233 4.0 39.1 1.0 NZ A:LYS232 4.3 45.2 1.0 CD A:GLN233 4.4 37.5 1.0 O A:GLN233 4.5 34.1 1.0 C A:THR231 4.6 51.9 1.0 CG A:LYS232 4.6 41.0 1.0 N A:LYS232 4.7 43.4 1.0 CB A:LYS232 4.7 38.1 1.0 OE1 A:GLN233 4.8 36.8 1.0 C A:GLN233 4.8 37.1 1.0 NE2 A:GLN233 4.9 37.4 1.0 CE A:LYS232 4.9 42.3 1.0

Chlorine binding site 2 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl603 b:35.6 occ:1.00 N A:PHE523 3.2 32.5 1.0 N A:VAL236 3.4 31.6 1.0 ND2 A:ASN238 3.4 30.0 1.0 CB A:PHE523 3.5 28.5 1.0 O A:VAL236 3.6 29.4 1.0 O A:HOH802 3.6 54.1 1.0 CB A:SER235 3.6 30.9 1.0 CA A:SER235 3.8 31.1 1.0 CG2 A:VAL236 3.9 28.3 1.0 CA A:PHE523 4.0 32.6 1.0 C A:SER235 4.1 32.4 1.0 C A:VAL522 4.2 31.5 1.0 CA A:VAL522 4.2 31.3 1.0 CA A:VAL236 4.3 31.0 1.0 CG A:ASN238 4.3 42.4 1.0 C A:VAL236 4.3 30.5 1.0 OD1 A:ASN238 4.4 44.3 1.0 CG1 A:VAL522 4.5 34.2 1.0 O A:PHE523 4.6 35.7 1.0 O A:HOH732 4.7 31.9 1.0 CB A:VAL236 4.7 31.9 1.0 CG A:PHE523 4.7 32.1 1.0 O A:PHE521 4.8 30.7 1.0 C A:PHE523 4.8 34.6 1.0 OG A:SER235 4.8 30.5 1.0 CB A:VAL522 5.0 32.0 1.0

Chlorine binding site 3 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl604 b:54.7 occ:1.00 OG1 A:THR284 3.2 35.2 1.0 N A:VAL285 3.2 28.9 1.0 CE A:MET279 3.6 32.8 1.0 CG1 A:VAL285 3.6 26.4 1.0 CA A:THR284 3.7 31.2 1.0 CB A:THR284 3.9 32.0 1.0 O A:HOH854 4.0 39.9 1.0 C A:THR284 4.0 30.7 1.0 CB A:VAL285 4.1 32.5 1.0 CD1 A:LEU326 4.1 30.9 1.0 CA A:VAL285 4.2 28.9 1.0 CD2 A:LEU326 4.5 29.9 1.0 SD A:MET279 4.5 35.3 1.0 CG1 B:VAL243 4.6 25.6 1.0 O A:THR283 4.8 31.1 1.0 N A:SER286 4.8 28.0 1.0 OG A:SER286 4.8 30.9 1.0 CG A:LEU326 4.8 36.2 1.0 CB B:VAL243 5.0 32.3 1.0 N A:THR284 5.0 28.6 1.0

Chlorine binding site 4 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:49.7 occ:1.00 NH2 A:ARG473 3.2 32.8 1.0 NH1 A:ARG473 3.2 32.1 1.0 CZ A:ARG473 3.6 36.1 1.0 CA A:THR231 4.7 52.8 1.0 N A:THR231 4.7 58.1 1.0 NE A:ARG473 5.0 34.6 1.0

Chlorine binding site 5 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:33.7 occ:1.00 OG A:SER528 3.1 31.5 1.0 N A:SER528 3.4 32.3 1.0 CB A:TYR531 3.7 31.8 1.0 CB A:SER528 3.7 30.3 1.0 CD1 A:TYR531 4.0 31.2 1.0 CA A:SER528 4.0 33.2 1.0 CA A:TYR531 4.0 33.7 1.0 N A:TYR531 4.1 32.6 1.0 CB A:VAL527 4.1 29.3 1.0 CG A:TYR531 4.3 31.3 1.0 C A:VAL527 4.4 32.6 1.0 O A:SER528 4.4 28.0 1.0 CA A:VAL527 4.4 29.4 1.0 CE1 A:TYR530 4.4 34.3 1.0 CD1 A:TYR530 4.5 35.0 1.0 C A:SER528 4.5 33.9 1.0 CG1 A:VAL527 4.7 27.6 1.0 C A:TYR530 4.9 32.7 1.0

Chlorine binding site 6 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl602 b:50.7 occ:1.00 OG1 B:THR284 3.0 33.7 1.0 N B:VAL285 3.3 29.8 1.0 O B:HOH849 3.6 38.2 1.0 CG1 B:VAL285 3.7 26.2 1.0 CE B:MET279 3.7 37.1 1.0 CA B:THR284 3.8 32.1 1.0 CB B:THR284 3.9 31.4 1.0 CD1 B:LEU326 4.0 31.3 1.0 C B:THR284 4.1 31.1 1.0 CB B:VAL285 4.2 31.3 1.0 CA B:VAL285 4.3 27.7 1.0 CD2 B:LEU326 4.4 30.1 1.0 CG1 A:VAL243 4.5 25.7 1.0 SD B:MET279 4.7 35.7 1.0 OG B:SER286 4.8 29.1 1.0 CG B:LEU326 4.8 36.9 1.0 N B:SER286 4.8 27.7 1.0 O B:THR283 4.9 31.9 1.0 CB A:VAL243 4.9 30.7 1.0

Chlorine binding site 7 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl603 b:48.6 occ:1.00 NH2 B:ARG473 3.2 34.2 1.0 NH1 B:ARG473 3.2 29.7 1.0 CZ B:ARG473 3.6 32.8 1.0 CB B:THR231 4.4 55.4 1.0 CG2 B:THR231 4.4 58.2 1.0 CA B:THR231 4.5 49.5 1.0 NE B:ARG473 5.0 30.7 1.0

Chlorine binding site 8 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl604 b:36.2 occ:1.00 N B:PHE523 3.2 29.8 1.0 ND2 B:ASN238 3.4 30.7 1.0 N B:VAL236 3.4 32.3 1.0 CB B:PHE523 3.5 28.4 1.0 O B:VAL236 3.6 30.5 1.0 CB B:SER235 3.7 33.1 1.0 CA B:SER235 3.9 32.0 1.0 CG2 B:VAL236 3.9 27.8 1.0 CA B:PHE523 3.9 31.7 1.0 CA B:VAL522 4.0 31.5 1.0 C B:VAL522 4.1 32.0 1.0 C B:SER235 4.2 30.8 1.0 CG B:ASN238 4.3 42.0 1.0 CA B:VAL236 4.3 29.9 1.0 C B:VAL236 4.4 32.1 1.0 OD1 B:ASN238 4.4 44.6 1.0 O B:PHE523 4.6 34.5 1.0 CB B:VAL522 4.6 33.6 1.0 O B:HOH716 4.6 32.9 1.0 CB B:VAL236 4.7 29.6 1.0 O B:PHE521 4.8 31.5 1.0 C B:PHE523 4.8 33.4 1.0 OG B:SER235 4.8 30.9 1.0 CG B:PHE523 4.8 30.2 1.0

Chlorine binding site 9 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl605 b:57.5 occ:1.00 N B:SER346 3.2 40.2 1.0 CB B:SER346 3.5 37.6 1.0 CD B:PRO345 3.6 32.8 1.0 OG B:SER346 3.7 41.5 1.0 CG2 B:THR344 3.8 29.1 1.0 N B:PRO345 3.9 37.3 1.0 CA B:SER346 3.9 42.6 1.0 CB B:PRO345 3.9 33.6 1.0 CG B:PRO345 4.1 31.5 1.0 C B:PRO345 4.1 40.7 1.0 CA B:PRO345 4.2 36.7 1.0 C B:THR344 4.6 35.7 1.0

Chlorine binding site 10 out of 11 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl606 b:48.5 occ:1.00 O B:HOH750 3.3 38.3 1.0 O B:HOH877 3.3 50.8 1.0 O B:HOH766 3.6 32.2 1.0 CA B:GLY474 3.8 26.8 1.0 N B:GLY474 4.3 31.2 1.0 O B:ARG473 4.3 31.9 1.0 C B:GLY474 4.3 31.9 1.0 N B:GLU475 4.5 30.9 1.0 C B:ARG473 4.5 30.9 1.0 CG B:GLU475 4.8 34.4 1.0

T.Kimura-Someya, M.Kato-Murayama, K.Katsura, N.Sakai, K.Murayama, K.Hanada, M.Shirouzu, Y.Someya. Lewis Fucose Is A Key Moiety For the Recognition of Histo-Blood Group Antigens By Gi.9 Norovirus, As Revealed By Structural Analysis. Febs Open Bio V. 12 560 2022.
ISSN: ESSN 2211-5463
PubMed: 35038379
DOI: 10.1002/2211-5463.13370