Sodium in PDB 5wke: Crystal Structure of Human CD1B in Complex with Ps

The structure of Crystal Structure of Human CD1B in Complex with Ps, PDB code: 5wke 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)	35.64 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.250, 78.550, 84.790, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.9

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

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CD1B in Complex with Ps (pdb code 5wke). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human CD1B in Complex with Ps, PDB code: 5wke:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human CD1B in Complex with Ps


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 Ps within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:48.6 occ:1.00 OH B:TYR80 2.4 30.3 1.0 O B:THR73 2.5 31.1 1.0 OD2 B:ASP78 3.0 37.7 1.0 CB B:ASP78 3.0 27.8 1.0 CE2 B:TYR80 3.1 22.4 1.0 CZ B:TYR80 3.2 27.5 1.0 CG B:ASP78 3.3 36.8 1.0 C B:THR73 3.6 29.8 1.0 N B:THR75 3.7 32.3 1.0 CG2 B:THR75 3.7 38.8 1.0 CA B:PRO74 3.8 29.6 1.0 OG1 B:THR75 3.8 35.6 1.0 C B:PRO74 3.9 33.8 1.0 O B:HOH309 4.0 28.8 1.0 N B:PRO74 4.1 29.3 1.0 CB B:THR75 4.2 37.6 1.0 OD1 B:ASP78 4.3 37.4 1.0 CD2 B:TYR80 4.4 21.7 1.0 CA B:ASP78 4.5 26.8 1.0 CA B:THR75 4.5 32.4 1.0 CE1 B:TYR80 4.5 23.8 1.0 O B:PRO74 4.6 32.5 1.0 CE B:LYS43 4.6 38.3 1.0 CA B:THR73 4.7 23.2 1.0 N B:THR73 4.8 21.7 1.0 CD2 B:PHE72 4.9 25.3 1.0 C B:ASP78 5.0 30.6 1.0 O B:ASP78 5.0 31.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human CD1B in Complex with Ps


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 Human CD1B in Complex with Ps within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:45.3 occ:1.00 O B:MET101 2.5 45.2 1.0 O A:HOH707 2.6 58.9 1.0 O A:HOH665 2.7 43.1 1.0 O B:ARG99 2.8 48.7 1.0 CE1 A:HIS207 3.5 17.9 1.0 C B:ARG99 3.7 48.1 1.0 C B:MET101 3.7 82.5 1.0 O A:HOH527 3.8 39.3 1.0 NE2 A:HIS207 3.9 17.6 1.0 O B:HOH352 3.9 23.6 1.0 O B:ASP98 4.1 39.3 1.0 N B:MET101 4.2 48.2 1.0 NH1 A:ARG246 4.3 47.5 1.0 O A:HOH586 4.3 25.0 1.0 O B:HOH331 4.4 37.4 1.0 CA B:ARG99 4.4 40.2 1.0 OG A:SER192 4.4 21.4 1.0 ND1 A:HIS207 4.4 18.4 1.0 C B:ASP100 4.5 51.6 1.0 N B:ASP100 4.5 46.6 1.0 CA B:MET101 4.5 68.8 1.0 O A:HOH618 4.6 22.0 1.0 CA B:ASP100 4.8 47.1 1.0 CB A:SER192 4.8 20.8 1.0 O B:ASP100 5.0 50.9 1.0 CD2 A:HIS207 5.0 17.4 1.0 NE1 A:TRP190 5.0 15.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human CD1B in Complex with Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human CD1B in Complex with Ps within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:38.5 occ:1.00 OG B:SER22 2.4 45.1 1.0 O B:ASN23 2.8 18.8 1.0 OE1 B:GLU71 3.0 57.3 1.0 N B:ASN23 3.3 20.0 1.0 C B:ASN23 3.6 19.8 1.0 CB B:SER22 3.6 30.0 1.0 CB B:GLU71 3.7 20.6 1.0 CL B:CL206 3.8 76.1 1.0 C B:SER22 3.8 25.8 1.0 CE1 B:PHE24 3.9 26.6 1.0 CD B:GLU71 3.9 60.8 1.0 CA B:ASN23 3.9 17.7 1.0 CG B:GLU71 3.9 28.4 1.0 CA B:SER22 4.1 25.1 1.0 CD1 B:PHE24 4.1 24.9 1.0 CA B:GLU71 4.4 17.8 1.0 O B:SER22 4.5 26.2 1.0 O B:PHE72 4.6 21.9 1.0 N B:PHE72 4.6 19.3 1.0 CZ B:PHE24 4.6 26.3 1.0 N B:PHE24 4.7 15.9 1.0 C B:GLU71 4.9 21.4 1.0 CG B:PHE24 4.9 20.8 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