Sodium in PDB 4jrx: Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex

The structure of Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jrx was solved by Y.C.Liu, J.Rossjohn, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.100, 78.408, 105.339, 90.00, 93.06, 90.00
R / Rfree (%)	20.5 / 25.7

The structure of Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex also contains other interesting chemical elements:

Iodine

(I)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep Complex (pdb code 4jrx). 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 CA5 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jrx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep 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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:49.0 occ:1.00 O A:GLY16 2.5 42.0 1.0 O A:ARG14 2.5 49.0 1.0 O A:GLY18 2.8 41.0 1.0 O A:HOH420 3.3 38.4 1.0 C A:ARG14 3.7 48.8 1.0 C A:GLY16 3.7 42.3 1.0 N A:GLY18 3.8 38.1 1.0 C A:GLY18 3.9 40.9 1.0 CB A:ARG14 4.2 45.7 1.0 O A:PRO15 4.3 45.5 1.0 C A:ARG17 4.3 41.6 1.0 C A:PRO15 4.3 45.6 1.0 CA A:ARG17 4.3 36.9 1.0 CA A:GLY18 4.4 37.0 1.0 CA A:ARG14 4.4 45.1 1.0 N A:ARG17 4.5 37.6 1.0 N A:GLY16 4.5 39.7 1.0 N A:PRO15 4.7 44.4 1.0 N A:ARG14 4.7 44.6 1.0 CA A:GLY16 4.7 38.9 1.0 CG A:ARG14 4.8 56.7 1.0 CA A:PRO15 4.8 43.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep 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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:27.3 occ:1.00 O D:GLY124 2.4 31.2 1.0 O D:GLN6 2.5 42.0 1.0 OG1 D:THR123 2.6 26.8 1.0 O D:GLN8 2.6 42.6 1.0 C D:GLN8 3.5 42.4 1.0 C D:GLY124 3.6 31.9 1.0 C D:GLN6 3.6 42.2 1.0 CA D:THR9 3.8 38.6 1.0 CB D:THR123 3.9 27.6 1.0 O E:HOH430 3.9 44.1 1.0 N D:THR9 4.0 39.3 1.0 CB D:GLN6 4.0 36.5 1.0 OG1 D:THR125 4.1 33.3 1.0 N D:GLY124 4.1 30.4 1.0 O D:ALA7 4.1 42.6 1.0 C D:THR123 4.1 34.5 1.0 C D:ALA7 4.2 43.0 1.0 OG1 D:THR9 4.4 40.8 1.0 N D:GLN8 4.4 37.7 1.0 O D:THR123 4.4 34.9 1.0 CA D:GLN6 4.4 35.5 1.0 CA D:GLY124 4.5 29.6 1.0 N D:THR125 4.5 27.8 1.0 CA D:THR123 4.5 29.3 1.0 N D:ALA7 4.6 39.5 1.0 CA D:GLN8 4.6 37.0 1.0 CB D:THR9 4.6 41.0 1.0 CA D:THR125 4.7 27.5 1.0 C D:THR9 4.8 42.8 1.0 CA D:ALA7 4.8 39.6 1.0 O D:THR9 4.9 41.7 1.0 CG2 D:THR123 5.0 17.1 1.0 CB D:THR125 5.0 34.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of CA5 Tcr-Hla B*3505-Lpep 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 CA5 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:30.0 occ:1.00 NE2 E:GLN234 2.6 50.5 1.0 NE E:ARG236 3.3 34.7 1.0 CD E:GLN234 3.6 59.1 1.0 NH1 E:ARG236 3.9 27.8 1.0 CG E:LYS127 3.9 42.1 1.0 O E:HOH404 4.0 44.2 1.0 O E:LYS127 4.0 33.6 1.0 CZ E:ARG236 4.0 36.6 1.0 CG E:GLN234 4.2 47.5 1.0 CD E:ARG236 4.3 32.7 1.0 CZ E:PHE130 4.5 31.9 1.0 OE1 E:GLN234 4.5 52.0 1.0 CA E:LYS127 4.7 32.3 1.0 CB E:GLN234 4.7 36.4 1.0 CB E:LYS127 4.8 34.0 1.0 CG E:ARG236 4.8 36.6 1.0 C E:LYS127 4.8 35.8 1.0 CE1 E:PHE130 5.0 33.5 1.0

Y.C.Liu, J.J.Miles, M.A.Neller, E.Gostick, D.A.Price, A.W.Purcell, J.Mccluskey, S.R.Burrows, J.Rossjohn, S.Gras. Highly Divergent T-Cell Receptor Binding Modes Underlie Specific Recognition of A Bulged Viral Peptide Bound to A Human Leukocyte Antigen Class I Molecule. J.Biol.Chem. V. 288 15442 2013.
ISSN: ISSN 0021-9258
PubMed: 23569211
DOI: 10.1074/JBC.M112.447185