Sodium in PDB 5l2j: Crystal Structure of Human CD1B in Complex with C36-Gmm

The structure of Crystal Structure of Human CD1B in Complex with C36-Gmm, PDB code: 5l2j was solved by S.Gras, A.Shahine, J.Le Nours, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.36 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.660, 78.110, 91.330, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.9

The structure of Crystal Structure of Human CD1B in Complex with C36-Gmm also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CD1B in Complex with C36-Gmm (pdb code 5l2j). 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 C36-Gmm, PDB code: 5l2j:

Sodium binding site 1 out of 1 in the Crystal Structure of Human CD1B in Complex with C36-Gmm


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 C36-Gmm within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:29.6 occ:1.00 O B:HOH336 3.2 28.3 1.0 OG B:SER90 3.3 33.2 1.0 N B:SER90 3.4 22.9 1.0 O B:HOH408 3.7 28.9 1.0 CB B:SER90 4.0 24.5 1.0 CD2 B:LEU89 4.0 23.1 1.0 CA B:LEU89 4.0 17.6 1.0 C B:LEU89 4.2 23.1 1.0 CA B:SER90 4.3 23.0 1.0 CB B:LEU89 4.4 17.3 1.0 O B:HOH323 4.7 30.1 1.0 N B:GLN91 4.7 22.6 1.0 O B:THR88 4.8 20.1 1.0 CG B:LEU89 4.9 21.0 1.0 O B:HOH355 4.9 32.5 1.0 O B:GLN91 4.9 22.3 1.0

S.Gras, I.Van Rhijn, A.Shahine, T.Y.Cheng, M.Bhati, L.L.Tan, H.Halim, K.D.Tuttle, L.Gapin, J.Le Nours, D.B.Moody, J.Rossjohn. T Cell Receptor Recognition of CD1B Presenting A Mycobacterial Glycolipid. Nat Commun V. 7 13257 2016.
ISSN: ESSN 2041-1723
PubMed: 27807341
DOI: 10.1038/NCOMMS13257