Sodium in PDB 5wkg: Crystal Structure of Human CD1B in Complex with Pa

The structure of Crystal Structure of Human CD1B in Complex with Pa, PDB code: 5wkg was solved by A.Shahine, S.Gras, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 2.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.190, 78.530, 84.710, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 22.4

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

Iodine	(I)	3 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CD1B in Complex with Pa (pdb code 5wkg). 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 Pa, PDB code: 5wkg:

Sodium binding site 1 out of 1 in the Crystal Structure of Human CD1B in Complex with Pa


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 Pa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:15.4 occ:1.00 O B:LEU89 2.3 13.1 1.0 O B:HIS86 2.4 14.4 1.0 OD1 B:ASN85 2.4 14.7 1.0 O B:HOH338 2.4 18.9 1.0 CG B:ASN85 3.4 23.9 1.0 C B:LEU89 3.4 14.0 1.0 C B:HIS86 3.4 13.0 1.0 ND2 B:ASN85 3.8 20.1 1.0 N B:HIS86 4.0 10.1 1.0 CA B:LEU89 4.1 10.1 1.0 N B:LEU89 4.1 10.7 1.0 N B:VAL87 4.2 8.9 1.0 CB B:LEU89 4.2 9.7 1.0 CA B:VAL87 4.2 9.2 1.0 O B:SER90 4.3 19.8 1.0 CA B:HIS86 4.3 9.0 1.0 C B:VAL87 4.4 15.8 1.0 C B:SER90 4.4 19.7 1.0 N B:SER90 4.4 13.4 1.0 O B:VAL87 4.5 17.6 1.0 CB B:ASN85 4.6 11.4 1.0 CA B:SER90 4.7 14.5 1.0 N B:GLN91 4.7 16.5 1.0 C B:ASN85 4.8 11.5 1.0 N B:THR88 4.9 9.8 1.0 CA B:ASN85 5.0 10.2 1.0

A.Shahine, I.Van Rhijn, T.Y.Cheng, S.Iwany, S.Gras, D.B.Moody, J.Rossjohn. A Molecular Basis of Human T Cell Receptor Autoreactivity Toward Self-Phospholipids. Sci Immunol V. 2 2017.
ISSN: ESSN 2470-9468
PubMed: 29054999
DOI: 10.1126/SCIIMMUNOL.AAO1384