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Chlorine in PDB 5wke: Crystal Structure of Human CD1B in Complex with Ps

Protein crystallography data

The structure of Crystal Structure of Human CD1B in Complex with Ps, PDB code: 5wke was solved by A.Shahine, S.Gras, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.64 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.250, 78.550, 84.790, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.9

Other elements in 5wke:

The structure of Crystal Structure of Human CD1B in Complex with Ps also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human CD1B in Complex with Ps (pdb code 5wke). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Human CD1B in Complex with Ps, PDB code: 5wke:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5wke

Go back to Chlorine Binding Sites List in 5wke
Chlorine binding site 1 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:30.5
occ:1.00
 O A:PHE88 3.9 30.7 1.0
CA A:PHE88 4.1 26.8 1.0
C A:PHE88 4.1 30.6 1.0
CA A:ARG140 4.1 21.6 1.0
CB A:ARG140 4.2 24.6 1.0
NE A:ARG140 4.3 34.2 1.0
CG A:ARG140 4.4 30.5 1.0
O A:ASP87 4.5 31.2 1.0
N A:ARG140 4.5 21.7 1.0
OG A:SER139 4.5 38.9 1.0
CB A:PHE88 4.8 27.5 1.0
CD2 A:PHE88 4.8 30.1 1.0
CG A:GLN89 4.9 61.3 1.0
C A:SER139 4.9 25.5 1.0
NH2 A:ARG140 4.9 41.8 1.0
N A:GLN89 5.0 27.8 1.0

Chlorine binding site 2 out of 7 in 5wke

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Chlorine binding site 2 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl416

b:26.8
occ:1.00
 O A:HOH598 3.0 33.1 1.0
O A:HOH603 3.1 31.3 1.0
N A:LEU191 3.2 15.2 1.0
CA A:TRP190 3.7 12.8 1.0
CB A:TRP190 4.0 12.5 1.0
C A:TRP190 4.0 16.4 1.0
CB A:LEU191 4.1 15.2 1.0
CG A:LEU191 4.1 19.5 1.0
CA A:LEU191 4.2 14.3 1.0
O A:LEU191 4.4 17.9 1.0
CD2 A:LEU275 4.6 17.9 1.0
CD1 A:LEU275 4.7 18.9 1.0
CD1 A:LEU191 4.8 20.0 1.0
C A:LEU191 4.8 17.9 1.0
O A:HOH583 4.8 28.0 1.0
O A:ALA189 4.9 15.0 1.0
N A:TRP190 5.0 12.6 1.0

Chlorine binding site 3 out of 7 in 5wke

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Chlorine binding site 3 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl417

b:42.5
occ:1.00
 N A:SER112 3.1 9.9 1.0
CE1 A:TYR163 3.6 19.8 1.0
O A:HOH645 3.7 46.6 1.0
O A:HOH581 3.7 20.9 1.0
O A:SER112 3.7 14.7 1.0
CG1 A:VAL111 3.7 20.4 1.0
CA A:VAL111 3.8 11.6 1.0
C A:VAL111 4.0 12.5 1.0
CA A:SER112 4.0 10.7 1.0
CD1 A:TYR163 4.1 20.6 1.0
CB A:SER112 4.2 13.4 1.0
CB A:VAL111 4.3 18.8 1.0
O A:HOH605 4.3 33.3 1.0
C A:SER112 4.3 15.1 1.0
OG A:SER112 4.5 13.7 1.0
O A:ILE110 4.6 14.8 1.0
O A:HOH544 4.6 40.4 1.0
CZ A:TYR163 4.8 25.7 1.0
CG2 A:VAL111 4.8 18.8 1.0
OH A:TYR163 5.0 30.5 1.0
N A:VAL111 5.0 9.8 1.0

Chlorine binding site 4 out of 7 in 5wke

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Chlorine binding site 4 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl418

b:48.4
occ:1.00
 NE2 A:GLN82 3.0 30.0 1.0
O A:THR22 3.2 39.0 1.0
C A:THR22 3.6 37.6 1.0
N A:ALA24 3.6 22.2 1.0
CB A:ALA24 3.8 20.2 1.0
CG A:GLN82 3.9 27.0 1.0
CD A:GLN82 3.9 38.5 1.0
C A:TRP23 3.9 28.9 1.0
N A:TRP23 3.9 33.4 1.0
CA A:TRP23 4.0 32.4 1.0
CA A:ALA24 4.3 19.8 1.0
CA A:THR22 4.4 33.9 1.0
O A:SER21 4.6 35.1 1.0
O A:TRP23 4.7 26.1 1.0
O A:ALA24 4.8 23.4 1.0

Chlorine binding site 5 out of 7 in 5wke

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Chlorine binding site 5 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl419

b:53.1
occ:1.00
 N A:GLU95 3.0 14.2 1.0
O2 A:EDO413 3.2 23.8 1.0
CA A:GLY119 3.4 17.2 1.0
O B:HOH337 3.6 28.9 1.0
CB A:GLU95 3.6 14.4 1.0
CA A:PHE94 3.8 14.3 1.0
C A:PHE94 3.8 16.3 1.0
CA A:GLU95 3.8 12.4 1.0
O A:GLU95 3.9 13.8 1.0
N A:GLY119 3.9 16.2 1.0
CE1 B:HIS33 4.1 15.9 1.0
C A:GLY119 4.3 22.9 1.0
C A:GLU95 4.4 14.8 1.0
CB A:PHE94 4.4 16.7 1.0
ND1 B:HIS33 4.5 15.8 1.0
C2 A:EDO413 4.5 29.1 1.0
C1 A:EDO413 4.8 32.8 1.0
O A:PRO93 4.8 20.3 1.0
O A:GLY119 4.8 24.8 1.0
O A:PHE94 4.9 17.8 1.0
N A:GLY120 4.9 16.8 1.0
N A:PHE94 4.9 15.6 1.0

Chlorine binding site 6 out of 7 in 5wke

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Chlorine binding site 6 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:66.2
occ:1.00
 O B:LYS50 3.2 30.9 1.0
N B:GLU71 3.6 16.4 1.0
OG1 B:THR70 3.7 24.8 1.0
CA B:THR70 3.8 15.3 1.0
O B:HOH357 3.8 37.5 1.0
CG B:GLU71 4.1 28.4 1.0
C B:LYS50 4.1 30.3 1.0
CG B:LYS50 4.1 37.8 1.0
C B:THR70 4.2 18.4 1.0
CD B:LYS50 4.2 46.3 1.0
CB B:THR70 4.3 21.9 1.0
CE B:LYS50 4.3 53.6 1.0
CG B:GLU52 4.4 34.0 1.0
CB B:GLU71 4.4 20.6 1.0
O B:TYR69 4.5 17.9 1.0
NZ B:LYS50 4.5 64.8 1.0
OE2 B:GLU71 4.5 54.9 1.0
CB B:LYS50 4.6 28.4 1.0
CA B:GLU71 4.6 17.8 1.0
CD B:GLU71 4.8 60.8 1.0
N B:VAL51 4.9 24.9 1.0
CA B:VAL51 4.9 22.8 1.0
N B:THR70 4.9 15.7 1.0
N B:GLU52 4.9 20.7 1.0
CA B:LYS50 5.0 26.4 1.0

Chlorine binding site 7 out of 7 in 5wke

Go back to Chlorine Binding Sites List in 5wke
Chlorine binding site 7 out of 7 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl206

b:76.1
occ:1.00
 NE2 B:HIS15 3.1 30.4 1.0
CD2 B:HIS15 3.5 29.6 1.0
O B:SER22 3.6 26.2 1.0
NA B:NA203 3.8 38.5 1.0
C B:SER22 3.9 25.8 1.0
CE1 B:PHE24 4.1 26.6 1.0
OG B:SER22 4.1 45.1 1.0
CA B:ASN23 4.1 17.7 1.0
N B:ASN23 4.2 20.0 1.0
CD1 B:PHE24 4.2 24.9 1.0
CE1 B:HIS15 4.2 30.3 1.0
CB B:SER22 4.4 30.0 1.0
C B:ASN23 4.6 19.8 1.0
CG B:HIS15 4.7 26.4 1.0
CA B:SER22 4.9 25.1 1.0
O B:ASN23 4.9 18.8 1.0

Reference:

A.Shahine, I.Van Rhijn, T.Y.Cheng, S.Iwany, S.Gras, D.B.Moody, J.Rossjohn. A Molecular Basis of Human T Cell Receptor Autoreactivity Toward Self-Phospholipids. Sci Immunol V. 2 2017.
ISSN: ESSN 2470-9468
PubMed: 29054999
DOI: 10.1126/SCIIMMUNOL.AAO1384
Page generated: Fri Jul 26 19:24:40 2024

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