Iodine in PDB 8glh: Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5

The structure of Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5, PDB code: 8glh was solved by R.Farquhar, J.Rossjohn, A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.13 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.447, 77.049, 91.445, 90, 90, 90
R / Rfree (%)	16.6 / 22.1

The structure of Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iodine atom in the Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5 (pdb code 8glh). 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 Endogenous Pc C40:5, PDB code: 8glh:
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 Endogenous Pc C40:5


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 Endogenous Pc C40:5 within 5.0Å range: probe atom residue distance (Å) B Occ A:I701 b:16.9 occ:0.81 N2 C:NAG2 3.6 20.0 1.0 CD1 A:LEU171 3.9 25.8 1.0 C1 C:FUC7 4.1 29.6 1.0 C3 C:NAG2 4.1 22.6 1.0 C2 C:NAG2 4.3 18.9 1.0 C6 C:NAG1 4.4 24.9 1.0 C8 C:NAG2 4.5 31.5 1.0 C7 C:NAG2 4.5 29.6 1.0 O5 C:FUC7 4.5 32.8 1.0 C1 C:NAG2 4.5 20.6 1.0 O3 C:NAG2 4.7 25.7 1.0 O6 C:NAG1 4.7 28.2 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5


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 Endogenous Pc C40:5 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:29.6 occ:0.66 O B:HOH424 2.9 32.6 1.0 O B:HOH317 3.1 32.4 1.0 N B:GLY45 3.5 34.5 1.0 CB B:ALA81 3.5 25.9 1.0 O B:GLU79 3.8 30.1 1.0 C B:GLU79 4.0 26.6 1.0 C B:TYR80 4.1 31.7 1.0 N B:ALA81 4.1 22.8 1.0 CB B:GLU79 4.2 33.2 1.0 CA B:GLY45 4.2 35.8 1.0 N B:ASN44 4.2 31.9 1.0 CB B:LEU42 4.3 30.9 1.0 N B:TYR80 4.3 25.5 1.0 CA B:TYR80 4.3 27.6 1.0 C B:ASN44 4.4 31.4 1.0 CA B:ASN44 4.4 31.1 1.0 CE B:LYS96 4.4 44.0 1.0 O B:TYR80 4.5 27.2 1.0 CA B:ALA81 4.5 23.3 1.0 O B:LEU42 4.6 26.7 1.0 CD1 B:LEU42 4.7 25.4 1.0 OE2 B:GLU79 4.7 44.9 1.0 CG B:LYS96 4.8 36.3 1.0 CA B:GLU79 4.8 28.3 1.0 C B:LEU42 4.8 25.9 1.0 CD B:LYS96 4.9 40.4 1.0 C B:LYS43 4.9 36.5 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5


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 Endogenous Pc C40:5 within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:38.9 occ:0.52 O B:HOH378 3.2 37.9 1.0 O B:HOH400 3.5 49.3 1.0 N B:SER90 3.9 31.4 1.0 OG B:SER90 4.0 56.3 1.0 CB B:SER90 4.4 45.0 1.0 CD2 B:LEU89 4.4 25.1 1.0 CA B:LEU89 4.6 28.1 1.0 CA B:SER90 4.7 40.3 1.0 C B:LEU89 4.8 29.3 1.0 CB B:LEU89 4.9 26.3 1.0 N B:GLN91 5.0 30.6 1.0 O B:HOH404 5.0 42.2 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