Sodium in PDB 5wki: Crystal Structure of PG90 Tcr-CD1B-Pg Complex

The structure of Crystal Structure of PG90 Tcr-CD1B-Pg Complex, PDB code: 5wki 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)	75.73 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.010, 82.970, 90.160, 90.00, 94.88, 90.00
R / Rfree (%)	21.2 / 25.2

The structure of Crystal Structure of PG90 Tcr-CD1B-Pg Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex (pdb code 5wki). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex, PDB code: 5wki:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex


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 PG90 Tcr-CD1B-Pg Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na307 b:63.5 occ:1.00 O D:ALA184 3.2 66.0 1.0 CB D:ALA184 3.7 65.3 1.0 CD2 D:PHE198 3.8 44.7 1.0 CE2 D:PHE198 3.8 47.2 1.0 CG D:PHE198 3.9 43.5 1.0 CZ D:PHE198 3.9 45.4 1.0 CA D:ALA184 4.0 64.6 1.0 C D:ALA184 4.0 66.1 1.0 CD1 D:PHE198 4.0 46.0 1.0 CE1 D:PHE198 4.1 46.7 1.0 CB D:PHE198 4.6 42.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of PG90 Tcr-CD1B-Pg Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of PG90 Tcr-CD1B-Pg Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na303 b:62.1 occ:1.00 O E:GLY3 3.0 46.5 1.0 O E:ASP24 4.0 38.7 1.0 O E:PRO25 4.0 38.1 1.0 C E:GLY3 4.2 46.4 1.0 OG E:SER5 4.3 41.5 1.0 C E:PRO25 4.5 38.6 1.0 CG E:ASP24 4.7 42.2 1.0 C E:ASP24 4.7 38.8 1.0 OD2 E:ASP24 4.8 36.0 1.0 N E:SER5 4.8 31.4 1.0 CB E:ASP24 4.8 34.6 1.0 CB E:SER5 4.9 33.7 1.0 N E:GLY3 4.9 50.0 1.0 CA E:ILE26 4.9 35.5 1.0 N E:ILE26 5.0 35.7 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