Chlorine in PDB 8dv4: Crystal Structure of the BC8B Tcr-CD1B-Pi Complex

The structure of Crystal Structure of the BC8B Tcr-CD1B-Pi Complex, PDB code: 8dv4 was solved by R.Farquhar, J.Rossjohn, A.Shahine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.07 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.088, 65.43, 101.581, 90, 102.26, 90
R / Rfree (%)	19.2 / 25.5

The structure of Crystal Structure of the BC8B Tcr-CD1B-Pi Complex also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Crystal Structure of the BC8B Tcr-CD1B-Pi Complex (pdb code 8dv4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the BC8B Tcr-CD1B-Pi Complex, PDB code: 8dv4:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the BC8B Tcr-CD1B-Pi Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the BC8B Tcr-CD1B-Pi Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:64.5 occ:1.00 O A:ASP234 2.9 40.3 1.0 N A:ASP234 3.4 46.4 1.0 N A:ARG246 3.7 44.3 1.0 CA A:GLY233 3.8 43.8 1.0 C A:ASP234 3.9 40.6 1.0 C A:GLY233 3.9 48.1 1.0 CD1 A:LEU236 3.9 40.1 1.0 CB A:ARG246 4.0 44.6 1.0 CA A:ASP234 4.2 42.6 1.0 CG A:ARG246 4.2 51.9 1.0 CG A:LEU236 4.3 36.7 1.0 CA A:LEU245 4.4 41.4 1.0 CA A:ARG246 4.4 38.0 1.0 NE2 B:GLN10 4.5 39.9 1.0 CE1 A:TYR244 4.5 50.2 1.0 C A:LEU245 4.5 44.3 1.0 NE A:ARG246 4.5 49.7 1.0 CD1 A:TYR244 4.6 44.6 1.0 CD1 A:LEU245 4.6 44.4 1.0 O A:ARG246 4.6 39.7 1.0 N A:GLY233 4.7 44.0 1.0 CB A:ASP234 4.7 47.1 1.0 CZ A:ARG246 4.8 57.3 1.0 O A:TYR244 4.8 37.4 1.0 NH2 A:ARG246 4.9 49.8 1.0 O A:GLY233 4.9 50.5 1.0 CD A:ARG246 5.0 51.0 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the BC8B Tcr-CD1B-Pi Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the BC8B Tcr-CD1B-Pi Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl303 b:83.5 occ:1.00 N E:HIS168 3.2 57.2 1.0 N E:SER169 3.2 57.4 1.0 CB E:SER169 3.7 63.3 1.0 CA E:HIS168 4.0 49.4 1.0 CA E:VAL167 4.0 51.3 1.0 C E:HIS168 4.1 52.8 1.0 CA E:SER169 4.1 59.2 1.0 C E:VAL167 4.1 52.7 1.0 CB E:HIS168 4.1 53.9 1.0 CB E:VAL167 4.3 45.3 1.0 CD2 E:HIS168 4.4 63.5 1.0 CG E:HIS168 4.6 61.0 1.0 CG1 E:VAL167 4.7 44.9 1.0 O E:SER169 4.9 51.0 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the BC8B Tcr-CD1B-Pi Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the BC8B Tcr-CD1B-Pi Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl304 b:62.1 occ:1.00 NH2 E:ARG111 3.2 57.7 1.0 O E:LEU112 3.3 48.5 0.4 O E:LEU112 3.3 45.1 0.6 OG1 E:THR113 3.6 41.5 1.0 CZ E:ARG111 3.8 62.9 1.0 NE E:ARG111 4.0 56.1 1.0 NE2 E:HIS155 4.0 44.7 1.0 O E:SER87 4.0 40.5 1.0 CG2 E:THR86 4.1 35.3 1.0 C E:LEU112 4.1 43.5 0.4 C E:LEU112 4.1 44.7 0.6 O E:HOH412 4.2 51.4 1.0 N E:SER87 4.2 40.3 1.0 N E:LEU112 4.3 40.6 0.4 N E:LEU112 4.3 39.3 0.6 C E:SER87 4.4 40.2 1.0 CB E:ARG111 4.4 42.6 1.0 OD1 E:ASP154 4.5 51.0 1.0 CA E:SER87 4.6 40.7 1.0 NH1 E:ARG111 4.7 66.5 1.0 CG2 E:VAL88 4.7 47.4 1.0 C E:ARG111 4.7 38.8 1.0 CD2 E:HIS155 4.8 40.5 1.0 CA E:ARG111 4.8 40.3 1.0 N E:THR113 4.8 44.0 1.0 CB E:THR113 4.9 42.0 1.0 CA E:LEU112 4.9 44.6 0.6 CA E:LEU112 4.9 38.7 0.4 C E:THR86 4.9 44.7 1.0 CG E:ARG111 4.9 49.7 1.0 CA E:THR113 5.0 42.1 1.0

R.Farquhar, I.Van Rhijn, D.B.Moody, J.Rossjohn, A.Shahine. Alpha Beta T-Cell Receptor Recognition of Self-Phosphatidylinositol Presented By CD1B. J.Biol.Chem. V. 299 02849 2023.
ISSN: ESSN 1083-351X
PubMed: 36587766
DOI: 10.1016/J.JBC.2022.102849