Sodium in PDB 6xqp: Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru

The structure of Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru, PDB code: 6xqp was solved by W.Awad, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.81 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.877, 113.433, 209.606, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.5

The structure of Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru (pdb code 6xqp). 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 Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru, PDB code: 6xqp:

Sodium binding site 1 out of 1 in the Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru within 5.0Å range: probe atom residue distance (Å) B Occ F:Na302 b:19.6 occ:1.00 ND2 F:ASN207 3.5 38.8 1.0 ND2 F:ASN210 3.6 34.0 1.0 CD1 D:ILE2 3.8 53.9 1.0 CD2 F:PHE204 3.9 41.3 1.0 CB F:ASN207 3.9 47.8 1.0 CA F:PHE204 4.1 52.8 1.0 CG F:ASN207 4.1 49.5 1.0 CG D:ARG4 4.2 38.2 1.0 O F:THR203 4.3 50.5 1.0 NE D:ARG4 4.4 45.6 1.0 CD D:ARG4 4.4 42.6 1.0 CE2 F:PHE204 4.4 51.6 1.0 CG F:PHE204 4.5 37.2 1.0 CG F:ASN210 4.6 38.9 1.0 CG1 D:ILE2 4.7 38.3 1.0 O F:PHE204 4.7 43.8 1.0 CB F:PHE204 4.7 36.9 1.0 N F:PHE204 4.7 57.4 1.0 OD1 F:ASN210 4.7 49.4 1.0 C F:THR203 4.8 48.6 1.0 C F:PHE204 4.9 42.4 1.0 CZ D:ARG4 5.0 45.6 1.0

W.Awad, E.W.Meermeier, M.L.Sandoval-Romero, J.Le Nours, A.H.Worley, M.D.Null, L.Liu, J.Mccluskey, D.P.Fairlie, D.M.Lewinsohn, J.Rossjohn. Atypical TRAV1-2 - T Cell Receptor Recognition of the Antigen-Presenting Molecule MR1. J.Biol.Chem. V. 295 14445 2020.
ISSN: ESSN 1083-351X
PubMed: 32817339
DOI: 10.1074/JBC.RA120.015292