Sodium in PDB 5wl1: Crystal Structure of Human CD1B in Complex with Pg

The structure of Crystal Structure of Human CD1B in Complex with Pg, PDB code: 5wl1 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)	30.34 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.889, 80.280, 92.700, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.6

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

Iodine	(I)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Human CD1B in Complex with Pg (pdb code 5wl1). 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 Human CD1B in Complex with Pg, PDB code: 5wl1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human CD1B in Complex with Pg


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 Pg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na420 b:23.5 occ:1.00 H A:GLY258 2.5 13.2 1.0 O A:TRP277 2.7 15.9 1.0 O A:LEU259 2.8 12.2 1.0 HA2 A:GLY258 3.0 8.8 1.0 N A:GLY258 3.2 11.2 1.0 N A:LEU259 3.3 12.6 1.0 C A:GLY258 3.3 13.3 1.0 H A:LEU259 3.3 13.2 1.0 CA A:GLY258 3.3 11.8 1.0 HB3 A:TYR276 3.4 12.2 1.0 H A:TRP277 3.4 11.9 1.0 HH11 A:ARG278 3.5 10.8 1.0 C A:LEU259 3.7 11.5 1.0 HD3 A:ARG278 3.7 9.2 1.0 HD2 A:TYR276 3.8 13.5 1.0 NH1 A:ARG278 3.8 13.3 1.0 C A:TRP277 3.8 14.1 1.0 N A:TRP277 3.9 11.4 1.0 HB3 A:TRP277 3.9 12.8 1.0 HH12 A:ARG278 4.0 11.2 1.0 O A:GLY258 4.0 13.0 1.0 CA A:LEU259 4.1 12.0 1.0 HA A:TYR276 4.2 10.8 1.0 HA A:ALA257 4.2 12.2 1.0 CA A:TRP277 4.3 11.2 1.0 CB A:TYR276 4.4 11.6 1.0 HA3 A:GLY258 4.4 12.9 1.0 C A:ALA257 4.4 14.2 1.0 C A:TYR276 4.5 12.2 1.0 CZ A:ARG278 4.5 13.9 1.0 HB3 A:SER260 4.5 12.3 1.0 CA A:TYR276 4.6 10.5 1.0 HA A:ARG278 4.6 12.7 1.0 CB A:TRP277 4.7 13.3 1.0 HB2 A:LEU259 4.7 12.8 1.0 CD A:ARG278 4.7 10.7 1.0 CD2 A:TYR276 4.7 14.6 1.0 N A:SER260 4.8 10.8 1.0 HA A:LEU259 4.8 11.6 1.0 NE A:ARG278 4.9 10.7 1.0 CA A:ALA257 4.9 13.5 1.0 N A:ARG278 4.9 12.5 1.0 O A:ALA256 5.0 18.2 1.0 HA A:SER260 5.0 10.6 1.0

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


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 Pg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:16.4 occ:1.00 HG B:SER52 2.1 13.8 1.0 O B:ASP53 2.7 11.8 1.0 HA B:LEU64 2.7 7.8 1.0 O B:HOH328 2.8 16.0 1.0 OG B:SER52 2.8 12.4 1.0 O B:TYR63 2.9 9.7 1.0 HD23 B:LEU64 2.9 14.4 1.0 HB3 B:SER55 3.1 7.8 1.0 HB2 B:SER52 3.1 13.3 1.0 H B:SER55 3.2 9.9 1.0 HB2 B:SER55 3.4 9.2 1.0 HE1 B:TYR63 3.5 12.5 1.0 CB B:SER52 3.5 12.3 1.0 HD1 B:TYR63 3.5 11.2 1.0 N B:SER55 3.6 9.2 1.0 CB B:SER55 3.7 9.7 1.0 HA B:LEU54 3.7 8.9 1.0 CA B:LEU64 3.7 8.8 1.0 HH2 A:TRP31 3.7 12.2 1.0 C B:TYR63 3.8 10.3 1.0 CD1 B:TYR63 3.8 10.7 1.0 CE1 B:TYR63 3.8 12.1 1.0 C B:ASP53 3.8 13.0 1.0 H B:LEU65 3.9 10.7 1.0 CD2 B:LEU64 4.0 12.6 1.0 C B:LEU54 4.0 11.0 1.0 N B:LEU64 4.1 10.4 1.0 HB3 B:SER52 4.2 10.0 1.0 CA B:SER55 4.2 9.2 1.0 CA B:LEU54 4.2 9.8 1.0 HD22 B:LEU64 4.4 9.6 1.0 O B:HOH340 4.4 31.5 1.0 N B:LEU54 4.5 9.7 1.0 C B:SER52 4.5 12.8 1.0 N B:LEU65 4.5 9.7 1.0 HD21 B:LEU64 4.6 13.7 1.0 C B:LEU64 4.6 10.6 1.0 N B:ASP53 4.6 12.2 1.0 CZ B:TYR63 4.6 12.7 1.0 HG B:LEU64 4.7 12.3 1.0 CH2 A:TRP31 4.7 11.8 1.0 CB B:LEU64 4.7 9.7 1.0 CA B:SER52 4.7 11.6 1.0 CG B:LEU64 4.7 11.9 1.0 CG B:TYR63 4.7 10.2 1.0 O B:LEU54 4.7 10.8 1.0 O B:SER52 4.7 12.1 1.0 O A:HOH929 4.8 25.0 1.0 H B:TYR63 4.8 6.0 1.0 HB3 B:LEU64 4.9 8.3 1.0 H B:ASP53 4.9 12.5 1.0 CA B:ASP53 4.9 10.7 1.0 HD12 B:LEU54 4.9 12.1 1.0 OG B:SER55 4.9 12.0 1.0 O B:HOH251 5.0 14.6 1.0 C B:SER55 5.0 9.3 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