Sodium in PDB 4jry: Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex

The structure of Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jry 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)	100.00 / 2.80
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	237.600, 237.600, 61.200, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.3

The structure of Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex (pdb code 4jry). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jry:

Sodium binding site 1 out of 1 in the Crystal Structure of SB47 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 SB47 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:44.5 occ:1.00 O B:ASN83 3.8 44.0 1.0 O B:ASP34 3.9 48.4 1.0 C B:ASP34 4.1 47.1 1.0 OE2 B:GLU36 4.1 71.7 1.0 CB B:ASP34 4.2 46.2 1.0 CA B:HIS84 4.2 37.7 1.0 N B:ILE35 4.4 41.5 1.0 C B:ASN83 4.4 43.4 1.0 C B:HIS84 4.4 42.3 1.0 N B:VAL85 4.4 36.3 1.0 CA B:ILE35 4.4 40.3 1.0 CG B:GLU36 4.5 53.3 1.0 N B:HIS84 4.6 38.8 1.0 N B:GLU36 4.7 42.1 1.0 C B:ILE35 4.7 46.4 1.0 CA B:ASP34 4.8 44.7 1.0 CD B:GLU36 4.8 83.7 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