Sodium in PDB 4qrp: Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr

The structure of Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr, PDB code: 4qrp was solved by S.Gras, R.Berry, I.S.Lucet, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.160, 252.190, 79.450, 90.00, 101.97, 90.00
R / Rfree (%)	20.6 / 24.8

The structure of Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr also contains other interesting chemical elements:

Iodine

(I)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr (pdb code 4qrp). 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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr, PDB code: 4qrp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ E:Na303 b:39.8 occ:1.00 CE E:LYS177 3.3 72.0 1.0 N G:MET0 3.6 59.7 1.0 NE2 F:GLN87 3.7 33.1 1.0 CG E:LYS177 3.7 52.0 1.0 I E:IOD302 3.8 67.6 0.9 CD E:LYS177 3.9 63.8 1.0 CB G:MET0 3.9 62.1 1.0 NZ E:LYS177 4.2 78.7 1.0 CA G:MET0 4.4 59.3 1.0 CD F:GLN87 4.7 45.2 1.0 CG F:GLN87 4.8 33.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ G:Na102 b:43.6 occ:1.00 CE G:MET0 2.8 68.0 1.0 NE2 G:GLN2 3.1 48.7 1.0 CG G:PRO32 3.6 33.7 1.0 CD G:PRO32 3.8 29.1 1.0 CD G:GLN2 4.1 55.6 1.0 CG G:GLN2 4.1 43.7 1.0 CA E:GLY176 4.4 27.6 1.0 CB G:PRO32 4.6 29.6 1.0 SD G:MET0 4.6 71.3 1.0 CG1 G:VAL85 4.6 31.2 1.0 O E:GLY176 4.8 32.8 1.0 CG2 G:VAL85 5.0 31.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr


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 Hla B*0801 in Complex with Hskkkcdel and DD31 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ L:Na303 b:55.6 occ:1.00 NH1 L:ARG218 3.1 42.9 1.0 CD L:ARG218 3.4 48.1 1.0 I L:IOD302 3.4 60.8 1.0 CZ L:ARG218 4.1 61.2 1.0 NE L:ARG218 4.2 51.0 1.0 CG L:ARG218 4.4 42.3 1.0 CB L:ARG218 4.8 36.7 1.0

U.K.Nivarthi, S.Gras, L.Kjer-Nielsen, R.Berry, I.S.Lucet, J.J.Miles, S.L.Tracy, A.W.Purcell, D.S.Bowden, M.Hellard, J.Rossjohn, J.Mccluskey, M.Bharadwaj. An Extensive Antigenic Footprint Underpins Immunodominant Tcr Adaptability Against A Hypervariable Viral Determinant. J.Immunol. 2014.
ISSN: ISSN 0022-1767
PubMed: 25355921
DOI: 10.4049/JIMMUNOL.1401357