Sodium in PDB 6c6c: Structure of Glycolipid Agsa[20,6P] in Complex with Mouse CD1D

The structure of Structure of Glycolipid Agsa[20,6P] in Complex with Mouse CD1D, PDB code: 6c6c was solved by D.M.Zajonc, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.10 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.525, 98.339, 55.310, 90.00, 106.25, 90.00
R / Rfree (%)	20 / 24.1

The binding sites of Sodium atom in the Structure of Glycolipid Agsa[20,6P] in Complex with Mouse CD1D (pdb code 6c6c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Glycolipid Agsa[20,6P] in Complex with Mouse CD1D, PDB code: 6c6c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Glycolipid Agsa[20,6P] in Complex with 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 Glycolipid Agsa[20,6P] in Complex with Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:36.8 occ:1.00 OE1 A:GLN99 2.6 26.6 1.0 N A:GLY122 3.0 30.5 1.0 O A:GLU97 3.0 30.3 1.0 O A:ALA119 3.2 25.5 1.0 N A:GLN121 3.4 27.7 1.0 C A:ALA119 3.5 26.1 1.0 CD A:GLN99 3.5 26.3 1.0 CA A:GLY122 3.6 27.9 1.0 C A:GLU97 3.7 29.0 1.0 N A:GLN99 3.7 25.9 1.0 C A:PHE120 3.7 26.3 1.0 N A:PHE120 3.7 26.7 1.0 CG A:GLN99 3.8 25.9 1.0 CA A:PHE120 3.9 26.6 1.0 CG A:GLU97 3.9 35.2 1.0 CB A:ALA119 3.9 26.1 1.0 C A:GLN121 4.0 30.7 1.0 CA A:ILE98 4.0 27.6 1.0 CB A:GLN99 4.0 25.3 1.0 CA A:GLN121 4.0 30.0 1.0 C A:ILE98 4.1 26.9 1.0 N A:ILE98 4.2 27.7 1.0 CB A:GLU97 4.2 32.6 1.0 CA A:ALA119 4.3 25.6 1.0 CE1 B:HIS31 4.3 46.2 1.0 O A:PHE120 4.4 26.8 1.0 CA A:GLN99 4.5 25.6 1.0 C A:GLY122 4.5 27.6 1.0 CA A:GLU97 4.6 31.4 1.0 N A:LYS123 4.6 29.6 1.0 NE2 A:GLN99 4.7 24.6 1.0 O A:ILE98 4.9 25.7 1.0

Sodium binding site 2 out of 2 in the Structure of Glycolipid Agsa[20,6P] in Complex with 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 Glycolipid Agsa[20,6P] in Complex with Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:46.8 occ:1.00 O B:TRP60 2.5 26.0 1.0 ND1 B:HIS31 2.9 46.4 1.0 C B:TRP60 3.1 27.8 1.0 CG B:HIS31 3.5 44.2 1.0 N B:SER61 3.6 29.0 1.0 CA B:SER61 3.6 28.6 1.0 CE1 B:HIS31 3.6 46.2 1.0 CA A:GLY122 3.7 27.9 1.0 OE1 A:GLN99 3.8 26.6 1.0 CB B:HIS31 3.8 41.3 1.0 CB B:TRP60 3.9 28.6 1.0 CE1 B:PHE62 4.0 28.1 1.0 CD1 B:PHE62 4.1 27.6 1.0 CA B:TRP60 4.2 28.0 1.0 NE2 A:GLN99 4.2 24.6 1.0 CD A:GLN99 4.4 26.3 1.0 O A:GLY122 4.4 27.1 1.0 O B:PHE30 4.5 30.7 1.0 CD2 B:HIS31 4.5 46.9 1.0 C B:SER61 4.5 28.9 1.0 NE2 B:HIS31 4.5 49.6 1.0 C A:GLY122 4.6 27.6 1.0 CB B:SER61 4.7 28.6 1.0 N B:PHE62 4.7 28.1 1.0 N A:GLY122 4.8 30.5 1.0 CA B:HIS31 4.8 37.6 1.0 O B:ASP59 4.9 30.6 1.0 CZ B:PHE62 5.0 28.1 1.0

D.M.Zajonc, J.Wang. Structure-Function Analysis of Sphingamides To Be Published.