Iodine in PDB 8glf: Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2

The structure of Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2, PDB code: 8glf was solved by A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.86 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.57, 77.98, 91.32, 90, 90, 90
R / Rfree (%)	17.6 / 23.1

The structure of Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2 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 Sphingomyelin C34:2 (pdb code 8glf). 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 Sphingomyelin C34:2, PDB code: 8glf:
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 Sphingomyelin C34:2


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 Sphingomyelin C34:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:22.4 occ:0.96 N2 C:NAG2 3.6 16.8 1.0 CD1 A:LEU171 3.7 29.1 1.0 C1 C:FUC7 4.1 35.8 1.0 C3 C:NAG2 4.2 22.8 1.0 C2 C:NAG2 4.3 25.1 1.0 O5 C:FUC7 4.4 35.5 1.0 C1 C:NAG2 4.4 22.4 1.0 C6 C:NAG1 4.4 21.5 1.0 C8 C:NAG2 4.6 14.9 1.0 C7 C:NAG2 4.6 21.6 1.0 O6 C:NAG1 4.7 21.8 1.0 O3 C:NAG2 4.8 22.9 1.0

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


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 Sphingomyelin C34:2 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:48.1 occ:0.69 O B:HOH308 3.3 39.6 1.0 N B:GLY45 3.3 38.0 1.0 CB B:ALA81 3.5 26.1 1.0 O B:HOH366 3.7 30.7 1.0 O B:GLU79 3.9 35.5 1.0 CA B:GLY45 3.9 36.6 1.0 C B:TYR80 4.0 34.1 1.0 C B:GLU79 4.0 32.6 1.0 N B:ALA81 4.0 32.6 1.0 CB B:GLU79 4.1 41.8 1.0 N B:ASN44 4.2 34.7 1.0 CB B:LEU42 4.2 32.8 1.0 N B:TYR80 4.2 32.8 1.0 C B:ASN44 4.2 40.2 1.0 CA B:TYR80 4.2 30.5 1.0 CA B:ASN44 4.3 37.0 1.0 O B:TYR80 4.4 35.2 1.0 CA B:ALA81 4.4 26.2 1.0 OE2 B:GLU79 4.5 58.4 1.0 CD1 B:LEU42 4.6 35.2 1.0 O B:LEU42 4.7 27.5 1.0 CA B:GLU79 4.7 34.8 1.0 C B:LEU42 4.8 33.7 1.0 C B:LYS43 4.9 39.1 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