Sodium in PDB 6cpl: Crystal Structure of DR11 Presenting the GAG293 Epitope

The structure of Crystal Structure of DR11 Presenting the GAG293 Epitope, PDB code: 6cpl was solved by C.Farenc, S.Gras, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.16 / 2.45
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	65.746, 65.746, 222.514, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 25.3

The binding sites of Sodium atom in the Crystal Structure of DR11 Presenting the GAG293 Epitope (pdb code 6cpl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of DR11 Presenting the GAG293 Epitope, PDB code: 6cpl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of DR11 Presenting the GAG293 Epitope


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 DR11 Presenting the GAG293 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:48.0 occ:1.00 O A:ARG50 3.5 42.1 1.0 N A:ALA52 3.7 33.5 1.0 C A:PHE51 3.8 38.7 1.0 O A:ALA52 3.8 31.2 1.0 C A:ALA52 3.8 33.4 1.0 CA A:ALA52 4.0 31.9 1.0 O A:PHE51 4.0 37.8 1.0 C A:ARG50 4.0 41.5 1.0 O A:GLY49 4.1 39.2 1.0 CA A:PHE51 4.3 37.4 1.0 N A:PHE51 4.4 37.8 1.0 N A:SER53 4.4 30.2 1.0 OG A:SER53 4.4 47.7 1.0 CB C:ARG299 4.4 49.3 1.0 CD C:ARG299 4.5 72.6 1.0 CB A:SER53 4.5 35.3 1.0 CA A:ARG50 4.9 36.7 1.0 C A:GLY49 4.9 39.6 1.0 O C:ARG299 4.9 47.3 1.0 CA A:SER53 5.0 30.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of DR11 Presenting the GAG293 Epitope


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 DR11 Presenting the GAG293 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:63.2 occ:1.00 O B:HOH362 3.4 43.7 1.0 O B:GLU176 3.6 36.3 1.0 CD B:PRO178 3.9 33.2 1.0 C B:GLU176 4.0 37.1 1.0 CA B:HIS177 4.1 33.0 1.0 O B:SER126 4.2 36.4 1.0 N B:HIS177 4.3 33.6 1.0 OG B:SER126 4.3 52.3 1.0 N B:PRO178 4.3 31.5 1.0 CG B:GLU128 4.4 49.5 1.0 CG B:PRO178 4.4 37.4 1.0 CA B:ILE127 4.4 33.4 1.0 C B:HIS177 4.4 35.5 1.0 N B:GLU128 4.5 36.2 1.0 C B:SER126 4.5 37.0 1.0 C B:ILE127 4.6 38.4 1.0 N B:ILE127 4.6 33.5 1.0 OE1 B:GLU128 4.7 68.6 1.0 CB B:GLU176 4.8 34.9 1.0 CB B:GLU128 4.8 37.5 1.0 CD B:GLU128 4.8 75.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of DR11 Presenting the GAG293 Epitope


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of DR11 Presenting the GAG293 Epitope within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:0.4 occ:1.00 O C:TYR301 2.2 34.2 1.0 CD1 A:PHE54 2.3 32.5 1.0 CA A:PHE54 2.6 28.0 1.0 CG A:PHE54 2.9 29.9 1.0 CB A:PHE54 3.0 29.2 1.0 N A:GLU55 3.1 29.4 1.0 C C:TYR301 3.2 35.0 1.0 CE1 A:PHE54 3.3 33.1 1.0 C A:PHE54 3.3 32.4 1.0 O A:SER53 3.4 30.5 1.0 N C:TYR301 3.4 34.2 1.0 CA C:TYR301 3.6 32.3 1.0 CB C:TYR301 3.6 32.4 1.0 N A:PHE54 3.7 28.8 1.0 C A:SER53 4.0 32.2 1.0 CD2 A:PHE54 4.1 31.1 1.0 O C:HOH502 4.1 36.8 1.0 CD1 C:PHE300 4.2 47.8 1.0 C C:PHE300 4.3 40.3 1.0 CA A:GLU55 4.3 29.3 1.0 CZ A:PHE54 4.3 32.0 1.0 N C:LYS302 4.3 31.7 1.0 O A:PHE54 4.5 32.4 1.0 CB C:PHE300 4.6 42.5 1.0 CE2 A:PHE54 4.7 33.6 1.0 CA C:PHE300 4.7 40.4 1.0 O A:GLU55 4.7 31.0 1.0 CB A:GLU55 4.7 30.9 1.0 CA C:LYS302 4.8 31.9 1.0 C A:GLU55 4.9 32.3 1.0 CG C:PHE300 4.9 44.6 1.0 CG C:TYR301 5.0 32.7 1.0

M.Galperin, C.Farenc, M.Mukhopadhyay, D.Jayasinghe, A.Decroos, D.Benati, L.L.Tan, L.Ciacchi, H.H.Reid, J.Rossjohn, L.A.Chakrabarti, S.Gras. CD4+T Cell-Mediated Hla Class II Cross-Restriction in Hiv Controllers. Sci Immunol V. 3 2018.
ISSN: ESSN 2470-9468
PubMed: 29884618
DOI: 10.1126/SCIIMMUNOL.AAT0687