Chlorine in PDB 8gle: Crystal Structure of Human CD1B in Complex with Lysosulfatide

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

Resolution Low / High (Å)	49.16 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.871, 79.525, 93.174, 90, 90, 90
R / Rfree (%)	18.8 / 22.9

The structure of Crystal Structure of Human CD1B in Complex with Lysosulfatide also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Human CD1B in Complex with Lysosulfatide (pdb code 8gle). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human CD1B in Complex with Lysosulfatide, PDB code: 8gle:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human CD1B in Complex with Lysosulfatide


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 Lysosulfatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:37.6 occ:1.00 O A:HOH598 3.2 31.0 1.0 NH2 A:ARG71 3.3 44.6 1.0 CG A:ARG71 3.7 30.2 1.0 CD A:ARG71 3.9 34.1 1.0 CL A:CL408 4.1 24.8 1.0 CZ A:ARG71 4.3 47.4 1.0 O A:HOH692 4.5 34.8 1.0 NE A:ARG71 4.5 43.5 1.0 CD2 A:PHE75 4.9 31.6 1.0 CA A:GLY45 5.0 32.2 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human CD1B in Complex with Lysosulfatide


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 Lysosulfatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:24.8 occ:1.00 O A:HOH598 3.0 31.0 1.0 O A:HOH573 3.2 31.4 1.0 NE1 A:TRP40 3.5 29.1 1.0 CA A:GLY45 3.7 32.2 1.0 O A:HOH692 4.1 34.8 1.0 CL A:CL407 4.1 37.6 1.0 O A:SER42 4.2 30.1 0.4 CA A:SER42 4.2 32.0 0.6 O A:SER42 4.2 30.0 0.6 CA A:SER42 4.2 31.6 0.4 N A:GLY45 4.3 27.1 1.0 CE2 A:TRP40 4.4 25.5 1.0 CG2 A:ILE74 4.4 22.3 1.0 CZ2 A:TRP40 4.5 28.7 1.0 CG A:ARG71 4.5 30.2 1.0 CD1 A:TRP40 4.6 19.9 1.0 C A:SER42 4.6 29.6 0.4 C A:SER42 4.7 28.9 0.6 CB A:SER42 4.7 27.5 0.6 CB A:SER42 4.8 27.8 0.4 O A:ASP41 4.8 25.5 1.0 OG A:SER42 4.8 28.4 0.6 CD1 A:ILE74 4.9 30.6 1.0 C A:GLY45 4.9 33.7 1.0 O A:HOH644 5.0 38.5 1.0 CB A:ILE74 5.0 29.1 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Human CD1B in Complex with Lysosulfatide


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 Lysosulfatide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:34.4 occ:1.00 N B:GLY45 3.2 66.0 1.0 CB B:ALA81 3.7 44.8 1.0 O B:GLU79 3.8 52.1 1.0 CA B:GLY45 3.9 65.5 1.0 N B:ASN44 4.0 53.4 1.0 C B:GLU79 4.1 53.7 1.0 C B:ASN44 4.1 60.9 1.0 CA B:ASN44 4.1 63.4 1.0 CE B:LYS96 4.1 75.6 1.0 CB B:GLU79 4.2 64.7 1.0 N B:ALA81 4.2 47.6 1.0 C B:TYR80 4.2 52.4 1.0 CB B:LEU42 4.3 52.8 1.0 CD B:LYS96 4.4 73.2 1.0 N B:TYR80 4.4 50.7 1.0 CA B:TYR80 4.4 49.4 1.0 NZ B:LYS96 4.5 74.2 1.0 OE1 B:GLU79 4.5 84.0 1.0 CA B:ALA81 4.6 48.8 1.0 O B:TYR80 4.6 53.7 1.0 O B:LEU42 4.7 37.5 1.0 CG B:LYS96 4.7 62.5 1.0 C B:LYS43 4.7 48.7 1.0 C B:LEU42 4.8 41.1 1.0 CA B:GLU79 4.8 57.7 1.0 CD1 B:LEU42 4.9 45.5 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