Iodine in PDB 8glg: Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1

The structure of Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1, PDB code: 8glg was solved by A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.95 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.074, 80.529, 92.979, 90, 90, 90
R / Rfree (%)	18.6 / 20.9

The structure of Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1 also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Nickel	(Ni)	1 atom

The binding sites of Iodine atom in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1 (pdb code 8glg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1, PDB code: 8glg:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1


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 Phosphatidylethanolamine C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I608 b:15.8 occ:0.87 N2 C:NAG2 3.7 19.6 1.0 CD1 A:LEU171 3.9 14.8 1.0 C3 C:NAG2 4.1 18.5 1.0 C1 C:FUC7 4.1 20.9 1.0 C2 C:NAG2 4.3 17.0 1.0 C1 C:NAG2 4.5 17.3 1.0 C6 C:NAG1 4.5 16.1 1.0 O5 C:FUC7 4.6 22.5 1.0 C8 C:NAG2 4.6 17.3 1.0 O3 C:NAG2 4.6 20.6 1.0 C7 C:NAG2 4.6 19.2 1.0 O6 C:NAG1 4.7 16.3 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1


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 Phosphatidylethanolamine C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:30.3 occ:0.60 O B:HOH440 3.4 41.3 1.0 N B:GLY45 3.5 32.6 1.0 CB B:ALA81 3.7 21.4 1.0 CB B:GLU79 3.9 33.1 1.0 O B:GLU79 4.0 28.6 1.0 C B:GLU79 4.0 29.4 1.0 N B:ASN44 4.0 31.2 1.0 C B:TYR80 4.1 25.8 1.0 N B:ALA81 4.1 21.4 1.0 N B:TYR80 4.2 24.5 1.0 CA B:ASN44 4.2 32.9 1.0 CA B:GLY45 4.3 31.6 1.0 CA B:TYR80 4.3 21.9 1.0 C B:ASN44 4.3 38.4 1.0 O B:TYR80 4.3 26.2 1.0 CE B:LYS96 4.4 60.0 1.0 CB B:LEU42 4.5 22.9 1.0 CA B:ALA81 4.6 20.4 1.0 CA B:GLU79 4.6 30.5 1.0 O B:LEU42 4.7 23.2 1.0 CG B:LYS96 4.8 34.0 1.0 CD B:LYS96 4.8 48.4 1.0 C B:LYS43 4.9 31.9 1.0 C B:LEU42 4.9 25.2 1.0 NZ B:LYS96 4.9 69.3 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