Iodine in PDB 5wkg: Crystal Structure of Human CD1B in Complex with Pa

The structure of Crystal Structure of Human CD1B in Complex with Pa, PDB code: 5wkg 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)	40.58 / 2.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.190, 78.530, 84.710, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 22.4

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

Chlorine	(Cl)	4 atoms
Sodium	(Na)	1 atom

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

Iodine binding site 1 out of 3 in the Crystal Structure of Human CD1B in Complex with Pa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Human CD1B in Complex with Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:I418 b:39.5 occ:0.70 CE A:LYS143 3.8 40.1 1.0 NZ A:LYS143 4.0 40.7 1.0 O A:PHE88 4.0 22.4 1.0 CA A:PHE88 4.1 16.8 1.0 CA A:ARG140 4.1 15.5 1.0 C A:PHE88 4.2 22.2 1.0 CB A:ARG140 4.2 18.4 1.0 OG A:SER139 4.3 30.9 1.0 O A:ASP87 4.4 21.5 1.0 NE A:ARG140 4.4 20.5 1.0 N A:ARG140 4.4 14.9 1.0 CG A:ARG140 4.4 19.8 1.0 CG A:GLN89 4.5 37.7 1.0 CD A:LYS143 4.8 44.8 1.0 C A:SER139 4.9 20.5 1.0 CB A:PHE88 4.9 17.0 1.0 CD1 A:PHE88 4.9 18.3 1.0 NH2 A:ARG140 5.0 22.8 1.0 CB A:GLN89 5.0 21.7 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of Human CD1B in Complex with Pa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Human CD1B in Complex with Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:I419 b:15.9 occ:0.95 O A:HOH518 3.5 24.8 1.0 N2 A:NAG403 3.5 14.1 1.0 CD1 A:LEU171 3.7 17.6 1.0 O A:HOH502 3.8 16.4 1.0 C1 A:FUC402 4.1 18.9 1.0 C3 A:NAG403 4.1 14.4 1.0 C2 A:NAG403 4.1 12.8 1.0 C6 A:NAG401 4.3 13.3 1.0 O5 A:FUC402 4.4 18.1 1.0 C1 A:NAG403 4.5 10.5 1.0 C7 A:NAG403 4.5 12.9 1.0 O6 A:NAG401 4.6 18.4 1.0 C8 A:NAG403 4.6 8.4 1.0 O3 A:NAG403 4.7 15.6 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of Human CD1B in Complex with Pa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Human CD1B in Complex with Pa within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:37.4 occ:0.60 N B:GLY45 3.2 23.2 1.0 O B:HOH379 3.6 33.4 1.0 CB B:ALA81 3.7 17.9 1.0 O B:HOH383 3.7 40.5 1.0 CA B:GLY45 3.8 22.1 1.0 O B:GLU79 3.8 23.0 1.0 N B:ASN44 3.9 22.2 1.0 C B:ASN44 4.0 26.7 1.0 CA B:ASN44 4.0 22.9 1.0 C B:GLU79 4.0 24.6 1.0 C B:TYR80 4.1 21.5 1.0 N B:ALA81 4.1 17.1 1.0 CB B:LEU42 4.1 13.2 1.0 CB B:GLU79 4.3 24.1 1.0 N B:TYR80 4.3 20.6 1.0 CA B:TYR80 4.3 19.1 1.0 O B:TYR80 4.5 21.5 1.0 O B:LEU42 4.5 18.8 1.0 CA B:ALA81 4.6 17.2 1.0 CD1 B:LEU42 4.6 15.5 1.0 C B:LEU42 4.6 19.4 1.0 C B:LYS43 4.7 23.8 1.0 CA B:GLU79 4.8 22.3 1.0 CE B:LYS96 4.8 66.0 1.0 N B:LYS43 4.9 15.7 1.0

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