Sodium in PDB 6c6f: Structure of Glycolipid Agsa[26,P5P] in Complex with Mouse CD1D

The structure of Structure of Glycolipid Agsa[26,P5P] in Complex with Mouse CD1D, PDB code: 6c6f 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)	32.00 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.627, 98.476, 55.431, 90.00, 106.21, 90.00
R / Rfree (%)	19.6 / 22.2

The binding sites of Sodium atom in the Structure of Glycolipid Agsa[26,P5P] in Complex with Mouse CD1D (pdb code 6c6f). 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[26,P5P] in Complex with Mouse CD1D, PDB code: 6c6f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Glycolipid Agsa[26,P5P] 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[26,P5P] in Complex with Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:29.6 occ:1.00 OE1 A:GLN99 2.6 21.1 1.0 N A:GLY122 2.9 21.8 1.0 O A:GLU97 3.1 21.3 1.0 O A:ALA119 3.2 18.3 1.0 N A:GLN121 3.4 22.8 1.0 C A:ALA119 3.5 19.0 1.0 CD A:GLN99 3.5 18.6 1.0 CA A:GLY122 3.6 21.7 1.0 C A:GLU97 3.7 22.4 1.0 N A:GLN99 3.7 17.5 1.0 C A:PHE120 3.7 21.3 1.0 CG A:GLN99 3.7 17.9 1.0 N A:PHE120 3.7 19.4 1.0 CB A:ALA119 3.8 17.9 1.0 CA A:PHE120 3.9 21.2 1.0 CG A:GLU97 3.9 30.1 1.0 C A:GLN121 3.9 24.4 1.0 CA A:ILE98 4.0 20.8 1.0 CA A:GLN121 4.0 24.5 1.0 CB A:GLN99 4.0 17.3 1.0 C A:ILE98 4.0 20.3 1.0 N A:ILE98 4.1 20.8 1.0 CB A:GLU97 4.2 26.7 1.0 CA A:ALA119 4.3 17.0 1.0 CE1 B:HIS31 4.3 35.5 1.0 O A:PHE120 4.4 19.9 1.0 CA A:GLN99 4.4 17.9 1.0 C A:GLY122 4.5 20.7 1.0 CA A:GLU97 4.6 24.5 1.0 N A:LYS123 4.6 20.7 1.0 NE2 A:GLN99 4.8 18.3 1.0 O A:ILE98 4.9 20.1 1.0

Sodium binding site 2 out of 2 in the Structure of Glycolipid Agsa[26,P5P] 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[26,P5P] in Complex with Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:33.2 occ:1.00 O A:PHE128 2.7 20.1 1.0 O A:HOH488 2.9 38.8 1.0 N A:LEU116 3.1 18.5 1.0 O A:LEU116 3.5 17.8 1.0 CA A:PHE115 3.6 20.5 1.0 CD2 A:HIS117 3.6 22.4 1.0 NE2 A:HIS117 3.7 24.4 1.0 C A:PHE128 3.9 18.9 1.0 C A:PHE115 3.9 19.8 1.0 CE3 A:TRP129 3.9 33.9 1.0 CB A:ARG127 4.0 20.2 1.0 C A:LEU116 4.0 17.7 1.0 CB A:PHE115 4.0 21.4 1.0 CD A:ARG127 4.0 23.9 1.0 CA A:LEU116 4.1 17.5 1.0 N A:PHE128 4.2 17.2 1.0 CG A:ARG127 4.4 21.7 1.0 O4 A:FUC308 4.5 30.9 1.0 CZ3 A:TRP129 4.6 35.1 1.0 O A:SER114 4.6 21.9 1.0 CA A:PHE128 4.6 17.7 1.0 CB A:LEU116 4.7 18.5 1.0 N A:PHE115 4.8 21.6 1.0 N A:TRP129 4.8 19.7 1.0 CA A:ARG127 4.8 18.7 1.0 CA A:TRP129 4.8 22.2 1.0 CB A:TRP129 4.9 25.0 1.0 N A:HIS117 4.9 16.8 1.0 CG A:HIS117 4.9 21.4 1.0 C A:ARG127 4.9 18.4 1.0 CD2 A:TRP129 5.0 31.6 1.0 NH1 A:ARG127 5.0 31.4 1.0

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