Sodium in PDB 6oor: Structure of 1B1 Bound to Mouse CD1D

The structure of Structure of 1B1 Bound to Mouse CD1D, PDB code: 6oor was solved by G.Ying, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.13 / 2.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	84.051, 160.964, 165.422, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.4

The binding sites of Sodium atom in the Structure of 1B1 Bound to Mouse CD1D (pdb code 6oor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of 1B1 Bound to Mouse CD1D, PDB code: 6oor:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of 1B1 Bound to Mouse CD1D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of 1B1 Bound to Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:50.5 occ:1.00 OE1 A:GLN99 2.8 30.0 1.0 N A:GLY122 3.1 37.7 1.0 O A:GLU97 3.1 30.2 1.0 O A:ALA119 3.2 38.6 1.0 C A:ALA119 3.4 36.1 1.0 N A:GLN121 3.5 35.3 1.0 C A:GLU97 3.6 33.9 1.0 CD A:GLN99 3.7 30.4 1.0 CA A:GLY122 3.7 38.0 1.0 N A:GLN99 3.7 33.6 1.0 N A:PHE120 3.7 37.0 1.0 CB A:ALA119 3.7 33.8 1.0 C A:PHE120 3.8 35.2 1.0 CG A:GLN99 3.8 31.9 1.0 CA A:PHE120 3.9 34.7 1.0 CA A:ILE98 3.9 32.2 1.0 C A:ILE98 4.0 33.2 1.0 N A:ILE98 4.0 31.3 1.0 CB A:GLN99 4.0 33.4 1.0 C A:GLN121 4.1 37.3 1.0 CB A:GLU97 4.1 39.1 1.0 CE1 B:HIS31 4.2 46.6 1.0 CA A:ALA119 4.2 33.6 1.0 CA A:GLN121 4.2 36.0 1.0 C A:GLY122 4.5 36.3 1.0 CA A:GLN99 4.5 33.1 1.0 O A:PHE120 4.5 32.7 1.0 N A:LYS123 4.5 37.3 1.0 CA A:GLU97 4.6 36.2 1.0 NE2 B:HIS31 4.8 44.3 1.0 O A:ILE98 4.8 30.4 1.0 NE2 A:GLN99 4.9 30.8 1.0

Sodium binding site 2 out of 4 in the Structure of 1B1 Bound to Mouse CD1D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of 1B1 Bound to Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:58.1 occ:1.00 O A:LEU150 2.7 36.9 1.0 O A:ASP153 3.0 46.7 1.0 OG A:SER157 3.1 51.0 1.0 NE1 A:TRP133 3.2 32.0 1.0 N A:SER157 3.4 37.8 1.0 CD1 A:TRP133 3.5 31.4 1.0 C A:LEU150 3.7 34.6 1.0 CB A:THR156 3.8 37.6 1.0 CA A:SER157 3.8 41.3 1.0 CG2 A:THR156 3.8 36.8 1.0 CB A:SER157 3.8 43.3 1.0 CG A:LEU150 3.9 34.1 1.0 CD1 A:LEU150 3.9 34.6 1.0 C A:THR156 4.0 36.5 1.0 CB A:ASP153 4.0 38.2 1.0 C A:ASP153 4.1 42.6 1.0 CA A:ASN151 4.3 34.9 1.0 N A:ASN151 4.3 34.2 1.0 CA A:THR156 4.4 38.0 1.0 CA A:ASP153 4.4 40.3 1.0 CE2 A:TRP133 4.5 32.8 1.0 N A:ASP153 4.6 39.4 1.0 CG A:ASP153 4.6 38.3 1.0 CA A:LEU150 4.6 32.9 1.0 O A:THR156 4.7 37.1 1.0 C A:ASN151 4.7 36.4 1.0 O A:ASN151 4.8 38.7 1.0 CB A:LEU150 4.8 33.8 1.0 OD1 A:ASN151 4.8 36.3 1.0 OD2 A:ASP153 4.8 38.1 1.0 CG A:TRP133 4.8 32.3 1.0 N A:THR156 4.9 38.1 1.0 CD2 A:LEU150 4.9 34.5 1.0 OG1 A:THR156 4.9 38.6 1.0

Sodium binding site 3 out of 4 in the Structure of 1B1 Bound to Mouse CD1D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of 1B1 Bound to Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:50.0 occ:1.00 O H:TRP112 2.6 42.7 1.0 N L:HIS55 3.1 44.1 1.0 NA L:NA302 3.2 44.4 1.0 N L:LEU38 3.2 38.4 1.0 O L:LEU38 3.4 39.8 1.0 CA L:TYR37 3.5 40.8 1.0 C L:TYR37 3.5 40.8 1.0 C L:LEU38 3.5 37.8 1.0 C H:TRP112 3.7 44.5 1.0 CA L:HIS55 3.8 46.5 1.0 CA L:LEU38 3.9 38.7 1.0 O L:HIS36 3.9 36.4 1.0 ND1 L:HIS55 3.9 47.0 1.0 CA L:TYR54 4.0 44.6 1.0 C L:TYR54 4.0 46.3 1.0 N L:SER39 4.0 38.9 1.0 CD2 L:TYR37 4.1 43.2 1.0 CB L:TYR54 4.1 43.2 1.0 CB L:SER39 4.1 36.0 1.0 CB L:TYR37 4.3 41.5 1.0 OG L:SER39 4.3 36.1 1.0 CA H:TRP112 4.3 43.7 1.0 O L:TYR37 4.3 39.4 1.0 OG1 L:THR96 4.3 43.5 1.0 CA L:SER39 4.5 36.3 1.0 CG L:TYR37 4.5 42.9 1.0 N L:TYR37 4.5 38.9 1.0 O H:TYR111 4.6 39.0 1.0 C L:HIS36 4.7 39.5 1.0 CE1 L:HIS55 4.7 45.1 1.0 CG L:HIS55 4.7 45.7 1.0 N L:ALA56 4.7 47.3 1.0 CB L:HIS55 4.8 46.3 1.0 C L:HIS55 4.8 47.4 1.0 CE2 L:TYR37 4.8 45.7 1.0 N H:PHE113 4.9 47.3 1.0

Sodium binding site 4 out of 4 in the Structure of 1B1 Bound to Mouse CD1D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of 1B1 Bound to Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ L:Na302 b:44.4 occ:1.00 OG L:SER39 2.6 36.1 1.0 OG1 L:THR96 2.8 43.5 1.0 O L:LEU94 2.9 42.1 1.0 NA L:NA301 3.2 50.0 1.0 N L:SER39 3.3 38.9 1.0 O L:TYR37 3.5 39.4 1.0 CB L:SER39 3.5 36.0 1.0 CG2 L:THR96 3.6 43.6 1.0 C L:TYR37 3.6 40.8 1.0 O H:TRP112 3.6 42.7 1.0 C L:LEU38 3.7 37.8 1.0 N L:THR96 3.7 45.6 1.0 CA L:LEU38 3.7 38.7 1.0 CB L:THR96 3.7 43.7 1.0 C L:LEU94 3.7 39.9 1.0 N L:LEU38 3.8 38.4 1.0 CA L:SER39 4.0 36.3 1.0 CG L:LEU94 4.1 37.0 1.0 C L:GLN95 4.2 45.9 1.0 CA L:GLN95 4.3 44.6 1.0 CA L:THR96 4.3 43.7 1.0 N L:GLN95 4.3 40.4 1.0 CB L:LEU94 4.4 36.4 1.0 CA L:TYR37 4.5 40.8 1.0 O L:LEU38 4.5 39.8 1.0 O H:TYR111 4.5 39.0 1.0 CD2 L:LEU94 4.5 38.4 1.0 C H:TRP112 4.6 44.5 1.0 CA L:LEU94 4.7 38.4 1.0 CB L:TYR37 4.8 41.5 1.0 CA H:PHE113 4.8 48.6 1.0 OH L:TYR41 4.9 38.7 1.0

G.Ying, J.Wang, T.Mallevaey, S.Van Calenbergh, D.M.Zajonc. Structural Basis of Nkt Cell Inhibition Using the T-Cell Receptor-Blocking Anti-CD1D Antibody 1B1. J.Biol.Chem. V. 294 12947 2019.
ISSN: ESSN 1083-351X
PubMed: 31296659
DOI: 10.1074/JBC.RA119.009403