Iodine in PDB 8dv3: Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1

The structure of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1, PDB code: 8dv3 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)	46.58 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.816, 78.628, 92.725, 90, 90, 90
R / Rfree (%)	19.2 / 25.3

The structure of Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Iodine atom in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol C34:1 (pdb code 8dv3). 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 Presenting Phosphatidylinositol C34:1, PDB code: 8dv3:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol 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 Presenting Phosphatidylinositol C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1206 b:23.0 occ:0.74 N2 C:NAG2 3.6 20.1 1.0 CD1 A:LEU171 3.7 18.5 1.0 C3 C:NAG2 4.0 27.6 1.0 O6 C:NAG1 4.1 29.4 1.0 C2 C:NAG2 4.2 21.7 1.0 C1 C:NAG2 4.5 24.9 1.0 C6 C:NAG1 4.5 26.7 1.0 O3 C:NAG2 4.5 26.5 1.0 C8 C:NAG2 4.5 20.1 1.0 C7 C:NAG2 4.6 30.6 1.0 O2 C:FUC7 4.8 36.1 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of Human CD1B Presenting Phosphatidylinositol 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 Presenting Phosphatidylinositol C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1209 b:126.5 occ:1.00 CA A:ARG140 3.9 31.3 1.0 CB A:ARG140 4.1 34.3 1.0 CG A:GLN89 4.2 53.6 1.0 CA A:PHE88 4.2 43.4 1.0 O A:PHE88 4.2 38.2 1.0 N A:ARG140 4.3 28.5 1.0 C A:PHE88 4.3 50.9 1.0 O A:ASP87 4.4 49.8 1.0 CG A:ARG140 4.4 34.5 1.0 CD A:ARG140 4.4 35.1 1.0 CD A:LYS143 4.4 40.9 1.0 OG A:SER139 4.7 50.5 1.0 C A:SER139 4.8 30.4 1.0 CB A:GLN89 4.9 48.8 1.0 O A:SER139 4.9 30.9 1.0 CD2 A:PHE88 4.9 37.8 1.0 CB A:PHE88 4.9 32.6 1.0

R.Farquhar, I.Van Rhijn, D.B.Moody, J.Rossjohn, A.Shahine. Alpha Beta T-Cell Receptor Recognition of Self-Phosphatidylinositol Presented By CD1B. J.Biol.Chem. V. 299 02849 2023.
ISSN: ESSN 1083-351X
PubMed: 36587766
DOI: 10.1016/J.JBC.2022.102849