Sodium 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:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the BC8B Tcr-CD1B-Pi Complex, PDB code: 8dv4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium 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 Sodium with other atoms in the Na 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:Na608 b:68.1 occ:1.00 OE1 A:GLU68 2.6 77.9 1.0 CD A:ARG71 3.3 62.8 1.0 CD A:GLU68 3.9 73.2 1.0 CA A:GLU68 4.2 48.0 1.0 O A:GLY45 4.2 56.1 1.0 CB A:ARG71 4.3 53.8 1.0 NE A:ARG71 4.3 85.2 1.0 CG A:ARG71 4.4 56.9 1.0 CB A:GLU68 4.4 57.8 1.0 CG A:GLU67 4.5 50.8 1.0 N A:GLU68 4.6 48.8 1.0 O A:GLU67 4.6 49.6 1.0 OE2 A:GLU68 4.7 80.5 1.0 C A:GLU67 4.7 46.1 1.0 CG A:GLU68 4.8 57.8 1.0 NH1 A:ARG71 4.9 77.5 1.0

Sodium 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 Sodium with other atoms in the Na 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 A:Na610 b:66.1 occ:1.00 OD2 B:ASP55 3.5 53.1 1.0 OD1 B:ASP55 3.9 45.3 1.0 CD2 A:LEU50 4.1 45.7 1.0 CG B:ASP55 4.1 41.4 1.0 O A:HOH742 4.2 54.9 1.0 CD1 A:ILE48 4.2 51.0 1.0 CG2 A:ILE48 4.5 46.9 1.0 O B:HOH317 4.9 43.8 1.0

Sodium 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 Sodium with other atoms in the Na 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 B:Na201 b:64.0 occ:1.00 O A:HOH771 2.8 57.8 1.0 OD1 B:ASN26 2.9 46.6 1.0 N A:ALA239 3.3 58.7 1.0 ND2 B:ASN26 3.4 55.5 1.0 CG B:ASN26 3.5 49.6 1.0 CB A:ASN238 3.6 49.0 1.0 OD1 A:ASN238 3.6 50.4 1.0 CA A:ASN238 3.7 48.0 1.0 CG A:ASN238 4.0 49.8 1.0 C A:ASN238 4.0 54.8 1.0 CB B:PHE24 4.1 53.5 1.0 CB B:ARG14 4.1 53.8 1.0 CB A:ALA239 4.2 51.9 1.0 CA A:ALA239 4.4 54.8 1.0 CG B:ARG14 4.5 61.7 1.0 CG B:PHE24 4.6 53.6 1.0 CD B:ARG14 4.6 61.0 1.0 CB B:TYR69 4.7 40.1 1.0 CD2 B:PHE24 4.9 57.2 1.0 CD2 B:TYR69 4.9 49.1 1.0 CG B:TYR69 4.9 47.5 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