Chlorine 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
Sodium	(Na)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Human D462-E4 Tcr in Complex with Human MR1-5-Op-Ru, PDB code: 6xqp:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl303 b:16.1 occ:1.00 NE2 F:GLN29 3.2 22.8 1.0 N F:LEU74 3.5 23.2 1.0 CB F:LEU74 3.8 28.1 1.0 CB F:ASN73 3.8 27.1 1.0 CG F:LEU74 3.9 21.9 1.0 CG F:GLN29 4.1 23.1 1.0 CD F:GLN29 4.1 28.8 1.0 OE1 A:GLN71 4.2 39.0 1.0 CA F:LEU74 4.2 20.1 1.0 CD1 F:LEU74 4.3 24.2 1.0 O F:HOH452 4.4 20.2 1.0 CA F:ASN73 4.5 22.6 1.0 C F:ASN73 4.5 24.4 1.0 O2 A:GOL302 4.5 55.5 1.0 CD A:GLN71 4.7 37.5 1.0 CG F:ASN73 4.7 25.2 1.0 CG A:GLN71 4.7 32.0 1.0 OD1 F:ASN73 4.7 31.7 1.0 CB F:GLN29 4.8 28.1 1.0 N F:THR75 4.9 27.6 1.0 CG2 F:THR75 5.0 22.6 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl304 b:32.9 occ:1.00 OD2 F:ASP99 2.9 47.4 1.0 OG1 F:THR31 3.4 28.4 1.0 O A:HOH419 3.5 31.1 1.0 CG F:ASP99 3.6 37.4 1.0 NE1 A:TRP69 3.6 24.6 1.0 N F:ASP99 3.8 25.2 1.0 O E:HOH405 4.0 46.9 1.0 CB F:THR31 4.2 22.7 1.0 CA F:GLY98 4.2 22.5 1.0 ND2 F:ASN104 4.2 34.4 1.0 CB F:ASP99 4.3 31.6 1.0 OD1 F:ASP99 4.3 40.2 1.0 ND2 E:ASN97 4.3 67.2 1.0 CG2 F:THR31 4.4 22.6 1.0 CD1 A:TRP69 4.4 22.6 1.0 SD F:MET32 4.4 55.6 1.0 CG F:MET32 4.5 26.6 1.0 CD2 A:LEU65 4.5 18.4 1.0 C F:GLY98 4.5 27.9 1.0 CE2 A:TRP69 4.5 20.8 1.0 CA F:ASP99 4.7 27.1 1.0 CE F:MET32 4.7 46.2 1.0 CZ2 A:TRP69 4.9 20.1 1.0 O5' A:2LJ301 4.9 34.2 0.4

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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 H:Cl303 b:19.7 occ:1.00 O H:HOH440 3.3 39.4 1.0 O C:HOH456 3.5 46.4 1.0 N H:LEU74 3.7 21.0 1.0 CB H:ASN73 3.8 19.6 1.0 CG H:GLN29 3.9 16.8 1.0 CB H:LEU74 3.9 12.7 1.0 NE2 H:GLN29 4.0 22.6 1.0 CG H:LEU74 4.1 14.7 1.0 NE2 C:GLN71 4.3 36.5 1.0 CA H:LEU74 4.4 17.8 1.0 O H:HOH449 4.4 34.3 1.0 O1 C:GOL304 4.5 64.5 1.0 CD H:GLN29 4.5 22.2 1.0 CD1 H:LEU74 4.5 16.9 1.0 CA H:ASN73 4.6 14.2 1.0 C H:ASN73 4.6 18.7 1.0 CG H:ASN73 4.6 23.6 1.0 OD1 H:ASN73 4.6 26.9 1.0 CB H:GLN29 4.7 19.1 1.0 CD C:GLN71 4.7 40.3 1.0 O2 C:GOL304 4.8 55.7 1.0 C1 C:GOL304 4.8 71.7 1.0 C3 C:GOL304 4.8 38.3 1.0 CG2 H:THR75 4.8 18.9 1.0 CG C:GLN71 4.9 29.3 1.0 O C:HOH450 4.9 45.6 1.0 N H:THR75 5.0 16.3 1.0

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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 H:Cl304 b:19.6 occ:1.00 O G:HOH403 2.6 40.9 1.0 OG1 H:THR31 3.2 27.1 1.0 OD2 H:ASP99 3.6 44.2 1.0 NE1 C:TRP69 3.6 25.7 1.0 O C:HOH411 3.6 23.2 1.0 N H:ASP99 3.7 17.3 1.0 CG H:ASP99 3.8 36.4 1.0 CA H:GLY98 3.9 17.3 1.0 CB H:THR31 4.0 22.1 1.0 ND2 G:ASN97 4.0 45.4 1.0 OD1 H:ASP99 4.1 43.1 1.0 ND2 H:ASN104 4.1 24.3 1.0 CD2 C:LEU65 4.2 25.1 1.0 C H:GLY98 4.3 18.6 1.0 CG2 H:THR31 4.3 23.0 1.0 CG H:MET32 4.4 25.8 1.0 CD1 C:TRP69 4.4 26.2 1.0 CB H:ASP99 4.4 24.2 1.0 SD H:MET32 4.5 28.9 1.0 CE2 C:TRP69 4.5 17.2 1.0 CA H:ASP99 4.7 24.0 1.0 CZ2 C:TRP69 4.9 20.8 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