Chlorine in PDB 6d64: Crystal Structure of Human CD1B in Complex with Popc

Protein crystallography data

The structure of Crystal Structure of Human CD1B in Complex with Popc, PDB code: 6d64 was solved by A.E.Shahine, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.13 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.981, 80.032, 92.766, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.1

Other elements in 6d64:

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

Iodine (I) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human CD1B in Complex with Popc (pdb code 6d64). 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 Popc, PDB code: 6d64:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6d64

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Chlorine binding site 1 out of 7 in the Crystal Structure of Human CD1B in Complex with Popc


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl419

b:20.8
occ:1.00
 O A:HOH627 2.8 27.1 1.0
O A:HOH572 3.1 26.6 1.0
NE1 A:TRP40 3.4 20.8 1.0
CA A:GLY45 3.8 17.1 1.0
O A:HOH816 3.9 26.6 1.0
O A:SER42 4.2 20.4 0.4
CA A:SER42 4.2 18.4 0.6
CA A:SER42 4.2 18.7 0.4
O A:SER42 4.3 19.6 0.6
CE2 A:TRP40 4.3 19.2 1.0
CG2 A:ILE74 4.3 22.1 1.0
N A:GLY45 4.3 18.0 1.0
CD1 A:TRP40 4.4 18.5 1.0
CZ2 A:TRP40 4.4 19.9 1.0
C A:SER42 4.7 20.0 0.4
C A:SER42 4.7 20.8 0.6
OG A:SER42 4.7 18.1 0.6
CB A:SER42 4.7 23.2 0.6
CG A:ARG71 4.8 17.3 1.0
O A:ASP41 4.8 16.6 1.0
CB A:SER42 4.8 21.4 0.4
CD1 A:ILE74 4.9 25.1 1.0
CB A:ILE74 4.9 18.3 1.0
O A:HOH746 5.0 28.3 1.0
C A:GLY45 5.0 20.2 1.0

Chlorine binding site 2 out of 7 in 6d64

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


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl420

b:28.0
occ:1.00
 O A:HOH648 3.1 28.4 1.0
N A:LEU191 3.3 15.7 1.0
CA A:TRP190 3.8 14.6 1.0
O A:HOH669 3.8 38.7 1.0
CB A:LEU191 4.0 14.9 1.0
CB A:TRP190 4.0 17.8 1.0
C A:TRP190 4.1 17.1 1.0
CG A:LEU191 4.1 19.4 1.0
CA A:LEU191 4.2 14.5 1.0
O A:LEU191 4.4 22.0 1.0
O A:ASN283 4.5 48.7 0.6
O A:HOH858 4.6 52.1 1.0
CD1 A:LEU275 4.6 24.7 1.0
CD2 A:LEU275 4.7 21.0 1.0
CD1 A:LEU191 4.8 18.6 1.0
C A:LEU191 4.8 19.8 1.0
O A:HOH881 4.8 37.7 1.0

Chlorine binding site 3 out of 7 in 6d64

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


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl421

b:65.9
occ:1.00
 OD2 A:ASP122 2.9 26.6 1.0
CD A:ARG115 3.2 28.6 1.0
NE A:ARG115 3.2 32.4 1.0
O B:HOH386 3.6 37.1 1.0
O A:HOH599 3.6 36.8 1.0
NZ B:LYS60 3.7 37.6 1.0
OD1 A:ASP122 3.7 28.1 1.0
CG A:ASP122 3.7 20.0 1.0
O B:LYS60 3.8 25.1 1.0
NE1 B:TRP62 4.0 16.9 1.0
CZ2 B:TRP62 4.0 15.7 1.0
CE2 B:TRP62 4.2 12.9 1.0
CZ A:ARG115 4.3 33.7 1.0
CG A:ARG115 4.4 18.5 1.0
O A:HOH579 4.4 33.5 1.0
CG B:LYS60 4.4 36.9 1.0
CB A:ARG115 4.6 15.8 1.0
NH1 A:ARG115 4.8 30.8 1.0
C B:LYS60 5.0 16.7 1.0

Chlorine binding site 4 out of 7 in 6d64

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


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl422

b:27.9
occ:1.00
 O A:HOH920 4.0 49.9 1.0
O A:HOH526 4.0 42.2 1.0
CG2 A:ILE160 4.0 26.5 1.0
CD1 A:ILE69 4.1 24.8 1.0
OG1 A:THR157 4.2 37.3 1.0
CG2 A:THR157 4.3 24.2 1.0
CB A:ILE160 4.4 23.2 1.0
CD2 A:LEU161 4.4 18.9 1.0
CD1 A:ILE160 4.5 26.3 1.0
CA A:THR157 4.6 32.1 1.0
CB A:THR157 4.7 24.8 1.0
O A:THR157 4.7 23.6 1.0
CG A:LEU161 4.7 19.1 1.0
O A:HOH820 4.9 31.4 1.0

Chlorine binding site 5 out of 7 in 6d64

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


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl423

b:19.0
occ:1.00
 NE2 A:GLN228 2.4 57.0 1.0
OE1 A:GLN228 2.6 62.4 1.0
CD A:GLN228 2.8 54.6 1.0
O A:HOH519 3.1 39.5 1.0
O A:HOH501 4.3 49.5 1.0
CG A:GLN228 4.3 39.7 1.0
CB A:GLN228 5.0 27.6 1.0

Chlorine binding site 6 out of 7 in 6d64

Go back to Chlorine Binding Sites List in 6d64
Chlorine binding site 6 out of 7 in the Crystal Structure of Human CD1B in Complex with Popc


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl424

b:19.9
occ:1.00
 O A:PHE88 3.8 32.3 1.0
CA A:PHE88 3.9 34.7 1.0
CD A:LYS143 3.9 47.5 1.0
C A:PHE88 4.0 38.9 1.0
CA A:ARG140 4.1 20.0 1.0
CG A:ARG140 4.2 28.4 1.0
CB A:ARG140 4.2 25.1 1.0
CE A:LYS143 4.3 54.9 1.0
O A:ASP87 4.3 43.7 1.0
NE A:ARG140 4.4 30.4 1.0
N A:ARG140 4.6 22.3 1.0
CB A:PHE88 4.6 35.3 1.0
CD2 A:PHE88 4.6 35.8 1.0
OG A:SER139 4.7 43.0 1.0
N A:GLN89 4.8 35.9 1.0
CG A:PHE88 4.8 35.9 1.0
CD A:ARG140 4.9 30.1 1.0
CG A:GLN89 4.9 36.9 1.0
CB A:GLN89 4.9 37.5 1.0

Chlorine binding site 7 out of 7 in 6d64

Go back to Chlorine Binding Sites List in 6d64
Chlorine binding site 7 out of 7 in the Crystal Structure of Human CD1B in Complex with Popc


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 Popc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:20.4
occ:1.00
 N B:GLY45 3.5 39.8 1.0
CB B:ALA81 3.7 23.4 1.0
CB B:GLU79 3.9 40.8 1.0
C B:TYR80 4.0 36.3 1.0
C B:GLU79 4.0 27.9 1.0
O B:GLU79 4.1 33.8 1.0
N B:TYR80 4.1 30.5 1.0
N B:ALA81 4.1 28.5 1.0
N B:ASN44 4.1 36.2 0.9
CA B:GLY45 4.2 35.6 1.0
CA B:TYR80 4.2 26.4 1.0
CA B:ASN44 4.3 39.0 0.8
O B:TYR80 4.3 31.2 1.0
C B:ASN44 4.3 38.3 1.0
CB B:LEU42 4.5 26.1 1.0
CA B:ALA81 4.5 25.8 1.0
CA B:GLU79 4.6 37.6 1.0
OE1 B:GLU79 4.7 76.1 1.0
CD B:LYS96 4.7 58.0 1.0
O B:LEU42 4.8 25.2 1.0
CG B:LYS96 4.8 47.8 1.0
C B:LYS43 4.9 31.7 1.0
CG B:GLU79 5.0 57.5 1.0
CD B:GLU79 5.0 68.1 1.0
C B:LEU42 5.0 27.6 1.0

Reference:

A.Shahine, P.Reinink, J.F.Reijneveld, S.Gras, M.Holzheimer, T.Y.Cheng, A.J.Minnaard, J.D.Altman, S.Lenz, J.Prandi, J.Kubler-Kielb, D.B.Moody, J.Rossjohn, I.Van Rhijn. A T-Cell Receptor Escape Channel Allows Broad T-Cell Response to CD1B and Membrane Phospholipids. Nat Commun V. 10 56 2019.
ISSN: ESSN 2041-1723
PubMed: 30610190
DOI: 10.1038/S41467-018-07898-0
Page generated: Sat Dec 12 12:52:29 2020

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