Chlorine 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:

Iodine	(I)	2 atoms
Nickel	(Ni)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1, PDB code: 8glg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl604 b:20.0 occ:1.00 O A:HOH868 2.2 72.2 1.0 O A:HOH778 2.9 20.4 1.0 O A:HOH815 3.1 26.1 1.0 NE1 A:TRP40 3.4 17.6 1.0 CA A:GLY45 3.8 17.7 1.0 O A:HOH995 3.9 26.6 1.0 O A:SER42 4.2 24.1 0.8 CG2 A:ILE74 4.2 17.0 1.0 O A:SER42 4.2 21.5 0.2 CA A:SER42 4.2 16.3 0.8 CE2 A:TRP40 4.3 17.9 1.0 CA A:SER42 4.3 14.6 0.2 CD1 A:TRP40 4.3 17.6 1.0 N A:GLY45 4.4 18.3 1.0 CZ2 A:TRP40 4.5 17.6 1.0 C A:SER42 4.7 21.0 0.8 C A:SER42 4.7 20.3 0.2 CB A:SER42 4.7 19.6 0.8 OG A:SER42 4.7 27.2 0.8 CG A:ARG71 4.8 17.2 1.0 O A:ASP41 4.8 16.2 1.0 CB A:ILE74 4.8 16.4 1.0 O A:HOH976 4.8 54.7 1.0 O A:HOH929 4.9 29.1 1.0 C A:GLY45 4.9 20.8 1.0 CD1 A:ILE74 5.0 20.9 1.0 CB A:SER42 5.0 16.9 0.2

Chlorine binding site 2 out of 4 in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl605 b:21.1 occ:1.00 O A:HOH846 2.3 85.6 1.0 O A:HOH782 4.2 49.2 1.0 CD A:GLN228 4.2 53.2 1.0 NE2 A:GLN228 4.3 38.9 1.0 CG A:GLN228 4.4 32.7 1.0 OE1 A:GLN228 4.6 48.9 1.0 CB A:GLN228 4.9 22.6 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:28.9 occ:1.00 O A:HOH948 2.8 52.2 1.0 O A:HOH767 3.2 27.3 1.0 O A:HOH819 3.3 42.7 1.0 N A:LEU191 3.3 15.7 1.0 CA A:TRP190 3.8 15.4 1.0 CB A:TRP190 4.0 15.4 1.0 C A:TRP190 4.0 18.4 1.0 O A:HOH806 4.1 42.3 1.0 CB A:LEU191 4.1 15.0 1.0 CG A:LEU191 4.2 19.1 1.0 CA A:LEU191 4.2 15.2 1.0 O A:LEU191 4.4 19.5 1.0 O A:HOH1061 4.6 40.4 1.0 CD2 A:LEU275 4.7 22.7 1.0 CD1 A:LEU275 4.8 23.7 1.0 C A:LEU191 4.8 19.3 1.0 CD1 A:LEU191 4.8 20.0 1.0 O A:ALA189 5.0 17.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human CD1B in Complex with Phosphatidylethanolamine C34:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl607 b:12.9 occ:1.00 O A:HOH702 2.9 29.4 1.0 O A:HOH1018 3.3 32.6 1.0 CH2 A:TRP243 3.4 17.2 0.4 N A:LYS214 3.7 15.4 1.0 CZ3 A:TRP243 3.8 16.2 0.4 CE2 A:TYR212 3.9 15.0 1.0 CB A:LYS214 4.1 16.6 1.0 CB A:PRO213 4.1 15.6 1.0 OH A:TYR212 4.2 16.7 1.0 CZ A:TYR212 4.2 16.0 1.0 CD A:PRO7 4.2 18.0 1.0 CA A:GLY6 4.3 16.9 1.0 CZ2 A:TRP243 4.4 17.8 0.4 CA A:PRO213 4.4 12.9 1.0 NE1 A:TRP243 4.4 17.0 0.6 N A:PRO7 4.4 17.0 1.0 C A:GLY6 4.5 20.3 1.0 CD2 A:TYR212 4.6 14.8 1.0 CA A:LYS214 4.6 14.4 1.0 C A:PRO213 4.6 17.8 1.0 CG A:PRO7 4.6 22.9 1.0 O A:HOH1062 4.8 38.0 1.0 CD1 A:LEU35 4.9 16.8 1.0 O A:HOH882 4.9 18.9 1.0 CE3 A:TRP243 5.0 14.9 0.4

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