Iodine in PDB 8gli: Crystal Structure of Human CD1B in Complex with Mycobacterial C85-Gmm

The structure of Crystal Structure of Human CD1B in Complex with Mycobacterial C85-Gmm, PDB code: 8gli was solved by G.Balaji, J.Rossjohn, A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.22 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.234, 76.601, 92.444, 90, 90, 90
R / Rfree (%)	20.6 / 26.7

The structure of Crystal Structure of Human CD1B in Complex with Mycobacterial C85-Gmm also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the Crystal Structure of Human CD1B in Complex with Mycobacterial C85-Gmm (pdb code 8gli). 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 Mycobacterial C85-Gmm, PDB code: 8gli:
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 Mycobacterial C85-Gmm


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 Mycobacterial C85-Gmm within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:25.9 occ:1.00 N2 C:NAG2 3.6 23.3 1.0 CD1 A:LEU171 3.9 28.3 1.0 C3 C:NAG2 4.1 24.5 1.0 O5 C:FUC7 4.3 44.1 1.0 C2 C:NAG2 4.3 26.6 1.0 C6 C:NAG1 4.3 37.0 1.0 C8 C:NAG2 4.6 26.7 1.0 C1 C:NAG2 4.6 29.9 1.0 C7 C:NAG2 4.6 36.0 1.0 O6 C:NAG1 4.7 50.0 1.0 O3 C:NAG2 4.7 25.9 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of Human CD1B in Complex with Mycobacterial C85-Gmm


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 Mycobacterial C85-Gmm within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:84.0 occ:1.00 O B:HOH351 2.9 38.6 1.0 N B:GLY45 3.4 52.9 1.0 CB B:ALA81 3.8 42.2 1.0 O B:GLU79 3.9 47.5 1.0 N B:ASN44 4.0 44.5 1.0 C B:ASN44 4.0 52.0 1.0 C B:GLU79 4.1 40.4 1.0 CA B:ASN44 4.1 48.5 1.0 CA B:GLY45 4.1 46.7 1.0 CB B:GLU79 4.1 56.9 1.0 N B:ALA81 4.2 37.0 1.0 C B:TYR80 4.2 39.6 1.0 N B:TYR80 4.3 47.5 1.0 CB B:LEU42 4.3 37.3 1.0 CA B:TYR80 4.4 48.8 1.0 O B:LEU42 4.5 42.8 1.0 CG B:LYS96 4.6 45.6 1.0 CA B:ALA81 4.6 38.8 1.0 O B:TYR80 4.7 42.2 1.0 CD B:LYS96 4.7 51.0 1.0 CD1 B:LEU42 4.7 43.0 1.0 CA B:GLU79 4.8 49.4 1.0 C B:LEU42 4.8 40.5 1.0 C B:LYS43 4.9 44.9 1.0 O B:ASN44 4.9 50.5 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of Human CD1B in Complex with Mycobacterial C85-Gmm


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 Mycobacterial C85-Gmm within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:74.3 occ:1.00 OG1 B:THR73 4.0 57.4 1.0 OE2 B:GLU71 4.3 51.2 1.0 O B:HOH311 4.5 48.5 1.0 CG B:GLU71 4.7 36.0 1.0 CA B:PHE72 4.7 40.4 1.0 CD B:GLU71 4.7 45.4 1.0 O B:GLU71 4.8 35.0 1.0 C B:PHE72 4.9 43.9 1.0 N B:THR73 4.9 46.1 1.0 C B:GLU71 5.0 34.2 1.0

S.Huang, A.Shahine, T.Y.Cheng, Y.L.Chen, S.W.Ng, G.R.Balaji, R.Farquhar, S.Gras, C.S.Hardman, J.D.Altman, N.Tahiri, A.J.Minnaard, G.S.Ogg, J.A.Mayfield, J.Rossjohn, D.B.Moody. CD1 Lipidomes Reveal Lipid-Binding Motifs and Size-Based Antigen-Display Mechanisms Cell(Cambridge,Mass.) V. 186 1 2023.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2023.08.022