Sodium in PDB 6c6e: Structure of Glycolipid Agsa[26,6P] in Complex with Mouse CD1D

The structure of Structure of Glycolipid Agsa[26,6P] in Complex with Mouse CD1D, PDB code: 6c6e 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)	50.01 / 2.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.221, 106.140, 107.301, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.1

The binding sites of Sodium atom in the Structure of Glycolipid Agsa[26,6P] in Complex with Mouse CD1D (pdb code 6c6e). 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[26,6P] in Complex with Mouse CD1D, PDB code: 6c6e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Glycolipid Agsa[26,6P] 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[26,6P] in Complex with Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:32.1 occ:1.00 OE1 A:GLN99 2.6 19.3 1.0 N A:GLY122 3.1 23.0 1.0 O A:ALA119 3.2 20.0 1.0 O A:GLU97 3.2 19.7 1.0 N A:GLN121 3.4 20.3 1.0 C A:ALA119 3.5 19.7 1.0 CD A:GLN99 3.5 19.3 1.0 C A:GLU97 3.6 21.2 1.0 N A:GLN99 3.6 19.3 1.0 C A:PHE120 3.7 19.8 1.0 N A:PHE120 3.7 19.7 1.0 CG A:GLN99 3.7 18.6 1.0 CA A:ILE98 3.8 19.3 1.0 CA A:PHE120 3.8 20.6 1.0 CA A:GLY122 3.8 22.6 1.0 C A:ILE98 3.9 19.2 1.0 CB A:ALA119 3.9 19.3 1.0 N A:ILE98 3.9 19.9 1.0 CB A:GLN99 4.0 18.8 1.0 C A:GLN121 4.0 23.2 1.0 CA A:GLN121 4.0 22.4 1.0 CB A:GLU97 4.1 22.1 1.0 CE1 B:HIS31 4.2 22.8 1.0 CA A:ALA119 4.3 19.0 1.0 O A:PHE120 4.4 20.5 1.0 CA A:GLN99 4.4 19.6 1.0 CA A:GLU97 4.5 22.6 1.0 C A:GLY122 4.6 22.0 1.0 N A:LYS123 4.6 22.4 1.0 O A:ILE98 4.7 18.5 1.0 NE2 B:HIS31 4.7 24.2 1.0 NE2 A:GLN99 4.8 18.6 1.0 O A:HOH471 5.0 23.6 1.0

Sodium binding site 2 out of 2 in the Structure of Glycolipid Agsa[26,6P] 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[26,6P] in Complex with Mouse CD1D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:35.1 occ:1.00 O A:HOH402 2.6 40.3 1.0 O A:TRP40 2.7 19.2 1.0 O A:THR26 2.7 18.7 1.0 NH1 A:ARG74 3.2 29.9 1.0 C A:THR26 3.5 20.7 1.0 CD A:ARG74 3.6 25.0 1.0 C A:TRP40 3.6 20.9 1.0 CA A:ASP27 3.7 21.3 1.0 CD2 A:TRP40 3.8 22.9 1.0 CG A:TRP40 3.8 22.5 1.0 N A:SER28 3.8 20.3 1.0 O A:SER41 3.8 19.6 1.0 C A:SER41 3.8 22.1 1.0 N A:ASP27 3.9 20.4 1.0 N A:ASN42 4.0 22.2 1.0 C A:ASP27 4.1 20.6 1.0 CE3 A:TRP40 4.1 22.8 1.0 CB A:TRP40 4.1 21.6 1.0 CZ A:ARG74 4.1 28.7 1.0 CG2 A:THR26 4.1 20.9 1.0 NE A:ARG74 4.2 26.4 1.0 CD1 A:TRP40 4.2 23.2 1.0 CE2 A:TRP40 4.3 23.2 1.0 OG A:SER28 4.3 23.9 1.0 CA A:ASN42 4.3 22.8 1.0 N A:SER41 4.4 21.3 1.0 CA A:SER41 4.4 21.6 1.0 CA A:TRP40 4.5 20.7 1.0 CB A:THR26 4.5 20.0 1.0 NE1 A:TRP40 4.5 24.9 1.0 CB A:SER28 4.6 21.1 1.0 CA A:THR26 4.6 20.7 1.0 CZ3 A:TRP40 4.7 23.9 1.0 CG A:ARG74 4.8 24.1 1.0 CA A:SER28 4.8 19.9 1.0 CZ2 A:TRP40 4.9 23.1 1.0

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