Sodium in PDB 8glh: Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5

The structure of Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5, PDB code: 8glh 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)	41.13 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.447, 77.049, 91.445, 90, 90, 90
R / Rfree (%)	16.6 / 22.1

The structure of Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5 also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5 (pdb code 8glh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5, PDB code: 8glh:

Sodium binding site 1 out of 1 in the Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human CD1B in Complex with Endogenous Pc C40:5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:22.3 occ:1.00 O B:ASP55 2.6 16.0 1.0 OG B:SER54 2.7 16.9 1.0 O B:TYR65 2.9 13.7 1.0 O B:HOH411 2.9 22.8 1.0 CB B:SER54 3.4 18.9 1.0 N B:SER57 3.7 13.6 1.0 CB B:SER57 3.7 15.1 1.0 CA B:LEU66 3.7 16.6 1.0 CE1 B:TYR65 3.7 16.2 1.0 C B:ASP55 3.7 17.1 1.0 CD1 B:TYR65 3.8 17.0 1.0 C B:TYR65 3.8 14.5 1.0 CD2 B:LEU66 3.9 15.0 1.0 C B:LEU56 4.0 16.4 1.0 N B:LEU66 4.1 12.2 1.0 CA B:LEU56 4.3 17.4 1.0 CA B:SER57 4.3 18.4 1.0 C B:SER54 4.4 20.3 1.0 N B:LEU67 4.4 12.8 1.0 N B:LEU56 4.4 15.9 1.0 C B:LEU66 4.5 16.6 1.0 CA B:SER54 4.5 16.0 1.0 O B:HOH423 4.6 35.2 1.0 N B:ASP55 4.6 21.1 1.0 CB B:LEU66 4.6 15.5 1.0 CH2 A:TRP31 4.6 16.0 1.0 CZ B:TYR65 4.7 17.9 1.0 O B:SER54 4.7 17.3 1.0 CG B:LEU66 4.7 17.5 1.0 CG B:TYR65 4.7 17.7 1.0 O A:HOH943 4.7 27.5 1.0 O B:LEU56 4.7 15.4 1.0 CA B:ASP55 4.8 22.1 1.0 OG B:SER57 4.9 14.8 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