Chlorine 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:

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

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2, PDB code: 8glf:
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 Sphingomyelin C34:2


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 Sphingomyelin C34:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:56.8 occ:1.00 CG2 A:ILE160 4.0 20.2 1.0 CG2 A:THR157 4.1 26.0 1.0 CD1 A:ILE69 4.2 37.0 1.0 CD1 A:ILE160 4.2 32.9 1.0 CB A:ILE160 4.4 30.8 1.0 CA A:THR157 4.7 23.2 1.0 OG1 A:THR157 4.7 25.3 1.0 CB A:THR157 4.7 25.2 1.0 O A:THR157 4.9 22.6 1.0 CG1 A:ILE160 4.9 28.5 1.0

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


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 Sphingomyelin C34:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:30.4 occ:1.00 O A:HOH606 2.6 31.0 1.0 NE1 A:TRP40 3.4 22.8 1.0 O A:HOH650 3.6 32.9 1.0 CA A:GLY45 3.8 24.8 1.0 O A:HOH641 4.1 27.4 1.0 CG2 A:ILE74 4.1 26.9 1.0 CE2 A:TRP40 4.2 19.4 1.0 CA A:SER42 4.3 23.6 1.0 CZ2 A:TRP40 4.4 17.5 1.0 N A:GLY45 4.4 20.9 1.0 CD1 A:TRP40 4.4 15.9 1.0 O A:SER42 4.5 29.7 1.0 CB A:SER42 4.6 28.8 1.0 CG A:ARG71 4.7 29.3 0.6 CD1 A:ILE74 4.7 40.4 1.0 CB A:ILE74 4.7 27.9 1.0 C A:SER42 4.8 27.4 1.0 CG A:ARG71 4.9 29.0 0.4 O A:ASP41 5.0 16.9 1.0 C A:GLY45 5.0 32.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2


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 Sphingomyelin C34:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:40.5 occ:1.00 N A:ALA189 3.5 19.2 1.0 O A:ALA189 3.8 15.2 1.0 CA A:GLU188 4.0 25.3 1.0 CG2 A:ILE273 4.2 27.6 1.0 C A:GLU188 4.3 20.7 1.0 CB A:GLU188 4.3 29.4 1.0 CA A:ALA189 4.4 21.0 1.0 O A:HOH579 4.4 35.1 1.0 CD1 A:ILE273 4.5 23.7 1.0 C A:ALA189 4.5 15.1 1.0 CB A:ALA189 4.6 17.6 1.0 CD2 A:LEU275 4.9 27.1 1.0 CG1 A:ILE273 5.0 27.7 1.0

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


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 Sphingomyelin C34:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:19.2 occ:1.00 O A:HOH642 3.0 23.9 1.0 O A:HOH643 3.3 44.0 1.0 CH2 A:TRP243 3.6 22.5 0.4 N A:LYS214 3.6 16.8 1.0 CB A:LYS214 3.8 28.3 1.0 CZ3 A:TRP243 3.9 21.0 0.4 CE2 A:TYR212 3.9 16.3 1.0 CB A:PRO213 4.1 22.3 1.0 CD A:PRO7 4.2 28.5 1.0 CZ A:TYR212 4.2 15.5 1.0 N A:PRO7 4.3 25.5 1.0 OH A:TYR212 4.3 17.0 1.0 CA A:GLY6 4.3 25.7 1.0 CA A:PRO213 4.3 19.4 1.0 CG A:PRO7 4.3 27.4 1.0 C A:GLY6 4.3 27.5 1.0 CA A:LYS214 4.3 26.7 1.0 C A:PRO213 4.5 20.0 1.0 CZ2 A:TRP243 4.6 24.8 0.4 CD2 A:TYR212 4.6 13.4 1.0 NE1 A:TRP243 4.6 22.2 0.6 CD A:LYS214 4.9 34.4 1.0 OD2 A:ASP33 4.9 39.3 1.0 CG A:LYS214 4.9 31.3 1.0 CA A:PRO7 4.9 17.3 1.0 CD1 A:LEU35 5.0 19.6 1.0 O A:HOH549 5.0 30.9 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