Sodium in PDB 6d64: Crystal Structure of Human CD1B in Complex with Popc

The structure of Crystal Structure of Human CD1B in Complex with Popc, PDB code: 6d64 was solved by A.E.Shahine, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.13 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.981, 80.032, 92.766, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.1

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

Iodine	(I)	2 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CD1B in Complex with Popc (pdb code 6d64). 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 Popc, PDB code: 6d64:

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


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 Popc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na427 b:54.4 occ:1.00 O A:HOH568 2.9 38.9 1.0 O A:HOH593 3.0 43.2 1.0 C2 A:EDO426 3.6 52.9 1.0 O A:HOH705 3.6 42.4 1.0 CB A:SER21 3.9 31.0 1.0 O A:HOH692 4.0 29.7 1.0 OG A:SER21 4.3 35.3 1.0 O2 A:EDO426 4.3 55.8 1.0 O A:GLN82 4.4 27.1 1.0 O A:HOH534 4.4 39.9 1.0 O A:HOH647 4.6 40.6 1.0 O A:SER21 4.7 28.3 1.0 O1 A:EDO426 4.8 59.9 1.0 C1 A:EDO426 4.8 55.0 1.0

A.Shahine, P.Reinink, J.F.Reijneveld, S.Gras, M.Holzheimer, T.Y.Cheng, A.J.Minnaard, J.D.Altman, S.Lenz, J.Prandi, J.Kubler-Kielb, D.B.Moody, J.Rossjohn, I.Van Rhijn. A T-Cell Receptor Escape Channel Allows Broad T-Cell Response to CD1B and Membrane Phospholipids. Nat Commun V. 10 56 2019.
ISSN: ESSN 2041-1723
PubMed: 30610190
DOI: 10.1038/S41467-018-07898-0