Chlorine in PDB 7vs9: Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X Antigen.

The structure of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X Antigen., PDB code: 7vs9 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)	35.21 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.2, 77.244, 103.526, 90, 124.2, 90
R / Rfree (%)	16.5 / 19.5

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

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

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 X Antigen. (pdb code 7vs9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X Antigen., PDB code: 7vs9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:46.1 occ:1.00 O A:HOH904 2.8 46.4 1.0 NH1 A:ARG473 3.1 32.4 1.0 NH2 A:ARG473 3.2 33.1 1.0 CZ A:ARG473 3.6 34.4 1.0 O A:HOH844 4.3 45.8 1.0 N A:THR231 4.8 52.4 1.0 NE A:ARG473 4.9 32.9 1.0 CA A:THR231 4.9 52.2 1.0

Chlorine binding site 2 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl603 b:50.7 occ:1.00 N A:GLN233 3.0 32.9 1.0 O A:HOH863 3.1 38.4 1.0 O A:THR231 3.5 43.5 1.0 CB A:GLN233 3.7 33.1 1.0 CA A:LYS232 3.8 40.1 1.0 CG A:GLN233 3.8 32.2 1.0 C A:LYS232 3.9 36.8 1.0 CA A:GLN233 3.9 34.2 1.0 CD A:LYS232 4.1 39.1 1.0 O A:GLN233 4.4 32.5 1.0 C A:THR231 4.4 46.2 1.0 CD A:GLN233 4.5 33.4 1.0 N A:LYS232 4.6 41.4 1.0 C A:GLN233 4.7 33.7 1.0 CB A:LYS232 4.8 35.0 1.0 CG A:LYS232 4.8 37.1 1.0 OE1 A:GLN233 4.9 35.7 1.0

Chlorine binding site 3 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl604 b:59.4 occ:1.00 N A:LYS232 3.3 41.4 1.0 CB A:LYS232 3.5 35.0 1.0 N A:THR231 3.6 52.4 1.0 O A:HOH789 3.6 42.1 1.0 CD A:PRO471 3.8 29.4 1.0 CG A:PRO471 3.9 33.5 1.0 CA A:LYS232 4.0 40.1 1.0 C A:THR231 4.3 46.2 1.0 CA A:THR231 4.3 52.2 1.0 CG2 A:THR231 4.4 46.0 1.0 CB A:THR231 4.6 47.0 1.0 O A:LYS232 4.7 36.0 1.0 CG A:LYS232 4.8 37.1 1.0 C A:LYS232 4.9 36.8 1.0

Chlorine binding site 4 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:36.2 occ:1.00 O A:HOH935 2.7 41.2 1.0 N A:PHE523 3.2 27.3 1.0 ND2 A:ASN238 3.3 32.1 1.0 N A:VAL236 3.4 27.2 1.0 CB A:PHE523 3.5 26.3 1.0 O A:VAL236 3.5 27.7 1.0 CB A:SER235 3.6 32.1 1.0 O A:HOH708 3.7 50.0 1.0 CA A:SER235 3.8 28.9 1.0 CA A:PHE523 4.0 27.3 1.0 O A:HOH765 4.0 44.6 1.0 CG2 A:VAL236 4.0 24.6 1.0 C A:SER235 4.1 28.6 1.0 CA A:VAL522 4.1 29.4 1.0 C A:VAL522 4.1 27.9 1.0 OD1 A:ASN238 4.1 47.3 1.0 CG A:ASN238 4.2 44.2 1.0 CG1 A:VAL522 4.3 34.4 1.0 CA A:VAL236 4.3 30.9 1.0 C A:VAL236 4.3 31.1 1.0 O A:PHE523 4.7 36.7 1.0 CB A:VAL236 4.8 30.4 1.0 OG A:SER235 4.8 30.1 1.0 CG A:PHE523 4.8 29.1 1.0 O A:HOH836 4.8 30.9 1.0 O A:PHE521 4.8 30.0 1.0 CB A:VAL522 4.8 30.3 1.0 C A:PHE523 4.9 32.7 1.0

Chlorine binding site 5 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:47.6 occ:1.00 OG1 A:THR284 3.1 33.2 1.0 O A:HOH946 3.4 43.5 1.0 N A:VAL285 3.4 28.5 1.0 O A:HOH959 3.5 40.1 1.0 O A:HOH963 3.5 34.8 1.0 CE A:MET279 3.5 34.6 1.0 O A:HOH885 3.6 37.7 1.0 CG1 A:VAL285 3.7 24.1 1.0 CA A:THR284 3.8 30.1 1.0 CB A:THR284 3.9 31.3 1.0 CD1 A:LEU326 4.0 32.9 1.0 CB A:VAL285 4.1 29.6 1.0 C A:THR284 4.1 29.3 1.0 CA A:VAL285 4.4 28.1 1.0 CD2 A:LEU326 4.6 29.6 1.0 CG1 B:VAL243 4.6 28.8 1.0 SD A:MET279 4.7 30.2 1.0 OG A:SER286 4.8 27.6 1.0 CG A:LEU326 4.8 34.5 1.0 N A:SER286 4.9 23.5 1.0 O A:THR283 4.9 27.6 1.0 CB B:VAL243 4.9 28.2 1.0 O A:HOH936 5.0 39.6 1.0

Chlorine binding site 6 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl607 b:53.4 occ:1.00 N A:SER346 3.2 37.1 1.0 CD A:PRO345 3.4 32.4 1.0 O A:HOH750 3.5 45.5 1.0 CB A:SER346 3.6 34.4 1.0 OG A:SER346 3.7 36.3 1.0 CG2 A:THR344 3.7 36.7 1.0 N A:PRO345 3.8 37.8 1.0 CB A:PRO345 3.8 34.7 1.0 CA A:SER346 4.0 40.0 1.0 CG A:PRO345 4.0 32.2 1.0 C A:PRO345 4.1 38.9 1.0 CA A:PRO345 4.1 36.6 1.0 C A:THR344 4.5 35.3 1.0

Chlorine binding site 7 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:43.0 occ:1.00 O A:HOH933 3.1 44.8 1.0 O A:HOH800 3.2 36.5 1.0 O A:HOH787 3.7 30.3 1.0 CA A:GLY474 3.7 28.0 1.0 N A:GLY474 4.3 31.9 1.0 C A:GLY474 4.3 31.2 1.0 O A:ARG473 4.4 31.0 1.0 N A:GLU475 4.4 30.7 1.0 C A:ARG473 4.5 30.8 1.0 CG A:GLU475 4.7 32.0 1.0

Chlorine binding site 8 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:48.7 occ:1.00 OG1 A:THR510 3.1 39.8 1.0 CG A:GLN513 3.6 37.5 1.0 N A:SER514 3.8 36.7 1.0 CA A:SER514 3.8 35.2 1.0 C A:GLN513 3.9 36.8 1.0 CB A:THR510 3.9 42.0 1.0 CB A:SER514 3.9 33.3 1.0 CB A:GLN513 3.9 36.5 1.0 CG2 A:THR510 3.9 39.9 1.0 O A:GLN513 4.0 37.9 1.0 CD A:GLN513 4.1 41.8 1.0 CA A:GLN513 4.5 36.3 1.0 OE1 A:GLN513 4.6 38.8 1.0 NE2 A:GLN513 4.6 45.4 1.0

Chlorine binding site 9 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl610 b:27.7 occ:1.00 OG A:SER528 3.2 29.8 1.0 N A:SER528 3.3 29.5 1.0 CB A:TYR531 3.6 26.5 1.0 CB A:SER528 3.8 28.2 1.0 CD1 A:TYR531 4.0 27.5 1.0 CA A:TYR531 4.0 28.8 1.0 CA A:SER528 4.0 30.8 1.0 N A:TYR531 4.1 30.7 1.0 CB A:VAL527 4.1 24.6 1.0 C A:VAL527 4.3 30.0 1.0 O A:SER528 4.3 29.5 1.0 CG A:TYR531 4.3 27.2 1.0 CA A:VAL527 4.3 28.1 1.0 CE1 A:TYR530 4.4 29.8 1.0 CD1 A:TYR530 4.5 28.3 1.0 C A:SER528 4.5 32.5 1.0 CG1 A:VAL527 4.7 26.6 1.0 C A:TYR530 4.9 32.0 1.0

Chlorine binding site 10 out of 16 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl602 b:36.5 occ:1.00 O B:HOH935 2.6 38.6 1.0 N B:PHE523 3.2 28.6 1.0 N B:VAL236 3.3 27.4 1.0 ND2 B:ASN238 3.4 32.7 1.0 CB B:PHE523 3.5 26.3 1.0 O B:VAL236 3.5 29.5 1.0 CB B:SER235 3.6 30.5 1.0 CA B:SER235 3.8 28.6 1.0 O B:HOH755 3.9 41.5 1.0 CG2 B:VAL236 3.9 24.7 1.0 CA B:PHE523 4.0 28.1 1.0 C B:SER235 4.1 27.4 1.0 CA B:VAL522 4.1 29.0 1.0 C B:VAL522 4.1 26.6 1.0 CA B:VAL236 4.3 29.3 1.0 C B:VAL236 4.3 30.4 1.0 CG B:ASN238 4.3 45.1 1.0 OD1 B:ASN238 4.3 48.3 1.0 CG1 B:VAL522 4.4 35.4 1.0 O B:PHE523 4.7 35.1 1.0 CB B:VAL236 4.7 27.9 1.0 OG B:SER235 4.7 29.4 1.0 O B:HOH834 4.8 29.8 1.0 CG B:PHE523 4.8 28.4 1.0 O B:PHE521 4.8 30.2 1.0 C B:PHE523 4.9 32.1 1.0 CB B:VAL522 4.9 29.1 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