Nickel 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:

Chlorine	(Cl)	4 atoms
Iodine	(I)	2 atoms

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2, PDB code: 8glf:

Nickel binding site 1 out of 1 in the Crystal Structure of Human CD1B in Complex with Sphingomyelin C34:2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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 B:Ni202 b:43.2 occ:1.00 O B:HOH340 3.2 51.3 1.0 OG B:SER90 3.7 46.2 1.0 N B:SER90 4.2 39.0 1.0 CD2 B:LEU89 4.2 36.5 1.0 CA B:LEU89 4.6 34.8 1.0 CB B:SER90 4.7 45.6 1.0 CE B:LYS93 4.8 63.5 1.0 C B:LEU89 4.9 33.6 1.0 O B:HOH356 5.0 32.6 1.0 CB B:LEU89 5.0 33.5 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