Sodium in PDB 6c15: CD1C in Complex with Phosphatidylcholine

The structure of CD1C in Complex with Phosphatidylcholine, PDB code: 6c15 was solved by K.S.Wun, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.56 / 3.21
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.255, 84.255, 366.833, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 24.2

The binding sites of Sodium atom in the CD1C in Complex with Phosphatidylcholine (pdb code 6c15). 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 CD1C in Complex with Phosphatidylcholine, PDB code: 6c15:

Sodium binding site 1 out of 1 in the CD1C in Complex with Phosphatidylcholine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CD1C in Complex with Phosphatidylcholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:25.0 occ:1.00 O A:GLU153 2.9 78.0 1.0 CB A:THR156 3.6 73.0 1.0 N A:GLU157 3.7 62.0 1.0 O A:GLY154 4.0 73.8 1.0 C A:GLU153 4.1 78.2 1.0 N A:THR156 4.2 64.1 1.0 CA A:THR156 4.2 62.0 1.0 CB A:GLU157 4.3 66.6 1.0 OG1 A:THR156 4.3 79.0 1.0 CG2 A:THR156 4.4 66.9 1.0 C A:THR156 4.4 63.7 1.0 CA A:GLU157 4.6 62.6 1.0 C A:GLY154 4.6 75.2 1.0 CA A:GLU153 4.9 73.8 1.0

K.S.Wun, J.F.Reijneveld, T.Y.Cheng, K.Ladell, A.P.Uldrich, J.Le Nours, K.L.Miners, J.E.Mclaren, E.J.Grant, O.L.Haigh, T.S.Watkins, S.Suliman, S.Iwany, J.Jimenez, R.Calderon, K.L.Tamara, S.R.Leon, M.B.Murray, J.A.Mayfield, J.D.Altman, A.W.Purcell, J.J.Miles, D.I.Godfrey, S.Gras, D.A.Price, I.Van Rhijn, D.B.Moody, J.Rossjohn. T Cell Autoreactivity Directed Toward CD1C Itself Rather Than Toward Carried Self Lipids. Nat. Immunol. V. 19 397 2018.
ISSN: ESSN 1529-2916
PubMed: 29531339
DOI: 10.1038/S41590-018-0065-7