Sodium in PDB 4pri: Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex

The structure of Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex, PDB code: 4pri was solved by L.Yu Chih, J.Rossjohn, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.70 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.580, 62.380, 100.460, 98.17, 94.59, 109.12
R / Rfree (%)	21.3 / 26.1

The structure of Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex (pdb code 4pri). 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 TK3 Tcr-Hla-B*35:08-Hpvg Complex, PDB code: 4pri:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex


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 TK3 Tcr-Hla-B*35:08-Hpvg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:45.8 occ:1.00 O B:ASP34 3.7 26.1 1.0 O B:ASN83 3.8 37.5 1.0 N B:VAL85 4.0 30.4 1.0 C B:ASP34 4.1 27.0 1.0 CA B:HIS84 4.1 32.4 1.0 C B:HIS84 4.2 35.6 1.0 CB B:ASP34 4.4 26.7 1.0 N B:ILE35 4.4 23.8 1.0 C B:ASN83 4.5 38.2 1.0 CA B:ILE35 4.5 23.5 1.0 N B:HIS84 4.6 33.9 1.0 CA B:VAL85 4.8 29.3 1.0 O B:HIS84 4.8 35.7 1.0 OE1 B:GLU36 4.8 53.0 1.0 CG B:GLU36 4.8 31.5 1.0 CA B:ASP34 4.9 24.0 1.0 C B:ILE35 4.9 27.7 1.0 CB B:VAL85 5.0 31.3 1.0 N B:GLU36 5.0 23.5 1.0 CD2 B:HIS84 5.0 36.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex


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 TK3 Tcr-Hla-B*35:08-Hpvg Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:30.6 occ:1.00 O D:ALA10 3.0 23.9 1.0 N D:ALA10 3.0 19.9 1.0 CB D:ALA10 3.5 20.1 1.0 CA D:ALA10 3.5 19.5 1.0 CG D:GLU9 3.6 28.9 0.5 C D:ALA10 3.7 22.5 1.0 N D:GLU9 3.7 20.9 1.0 CB D:PRO8 3.7 16.9 1.0 CL D:CL302 4.0 45.7 1.0 C D:GLU9 4.1 23.7 1.0 C D:PRO8 4.2 23.9 1.0 CA D:GLU9 4.3 20.2 1.0 CA D:PRO8 4.4 16.4 1.0 OE2 D:GLU9 4.4 39.9 0.5 CB D:GLU9 4.5 21.1 1.0 CD D:GLU9 4.5 40.7 0.5 CG D:PRO8 4.9 19.6 1.0 N D:LEU11 5.0 15.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of TK3 Tcr-Hla-B*35:08-Hpvg Complex


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 TK3 Tcr-Hla-B*35:08-Hpvg Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:29.3 occ:1.00 CB E:THR7 3.9 25.1 1.0 CG E:PRO8 4.0 31.1 1.0 CB E:PRO8 4.0 26.1 1.0 CA E:PRO8 4.1 24.2 1.0 N E:PRO8 4.1 25.3 1.0 C E:THR7 4.5 29.4 1.0 CD E:PRO8 4.5 27.1 1.0 OG1 E:THR7 4.5 26.6 1.0 CG2 E:THR7 4.6 16.9 1.0 CA E:THR7 4.7 24.2 1.0

Y.C.Liu, Z.Chen, M.A.Neller, J.J.Miles, A.W.Purcell, J.Mccluskey, S.R.Burrows, J.Rossjohn, S.Gras. A Molecular Basis For the Interplay Between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism. J.Biol.Chem. V. 289 16688 2014.
ISSN: ISSN 0021-9258
PubMed: 24759101
DOI: 10.1074/JBC.M114.563502