Sodium in PDB 7n4k: 6218 Tcr in Complex with H2-Db Pa 224

The structure of 6218 Tcr in Complex with H2-Db Pa 224, PDB code: 7n4k was solved by C.Szeto, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.07 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.14, 72.53, 107.72, 90, 101.36, 90
R / Rfree (%)	18.6 / 21.4

The binding sites of Sodium atom in the 6218 Tcr in Complex with H2-Db Pa 224 (pdb code 7n4k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 6218 Tcr in Complex with H2-Db Pa 224, PDB code: 7n4k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 6218 Tcr in Complex with H2-Db Pa 224


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 6218 Tcr in Complex with H2-Db Pa 224 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:50.1 occ:1.00 O D:GLN58 2.8 31.6 1.0 O A:HOH303 3.5 46.2 1.0 OE1 D:GLN59 3.6 47.5 1.0 O D:HOH460 3.6 32.5 1.0 C D:GLN58 3.7 30.4 1.0 CB D:GLN59 3.8 27.9 1.0 O D:HOH439 3.8 23.9 1.0 O D:ASN66 3.9 27.5 1.0 N D:ASN66 4.1 27.4 1.0 N D:GLN59 4.4 25.6 1.0 CA D:GLN59 4.4 26.8 1.0 CD D:GLN59 4.4 49.0 1.0 C D:GLN59 4.5 30.5 1.0 CG D:GLN59 4.6 22.5 1.0 CA D:GLN58 4.6 23.8 1.0 CB D:GLN58 4.6 25.4 1.0 C D:ASN66 4.7 28.1 1.0 OE2 A:GLU154 4.7 29.6 0.9 N D:GLN58 4.8 22.0 1.0 CA D:ASN66 5.0 26.3 1.0

Sodium binding site 2 out of 4 in the 6218 Tcr in Complex with H2-Db Pa 224


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 6218 Tcr in Complex with H2-Db Pa 224 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:39.9 occ:1.00 O D:HOH457 2.8 35.1 1.0 O D:HOH403 3.0 29.2 1.0 CA D:GLY30 3.6 19.5 1.0 CD D:ARG84C 3.9 19.3 1.0 NH1 D:ARG84C 4.2 21.6 1.0 O D:GLY30 4.5 22.1 1.0 N D:GLY30 4.5 20.1 1.0 C D:GLY30 4.6 22.6 1.0 NE D:ARG84C 4.6 18.0 1.0 NE2 D:GLN58 4.7 43.7 1.0 CZ D:ARG84C 4.7 26.4 1.0 O A:HOH338 4.9 34.2 1.0

Sodium binding site 3 out of 4 in the 6218 Tcr in Complex with H2-Db Pa 224


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 6218 Tcr in Complex with H2-Db Pa 224 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:24.5 occ:1.00 O E:HOH473 2.5 41.8 1.0 ND2 E:ASN212 3.1 29.1 1.0 ND2 E:ASN215 3.2 25.6 1.0 CD2 E:PHE209 3.7 21.3 1.0 CB E:ASN212 3.9 20.7 1.0 CG E:ASN212 3.9 30.9 1.0 CE2 E:PHE209 4.1 24.3 1.0 CG E:ASN215 4.1 31.1 1.0 OD1 E:ASN215 4.1 21.7 1.0 CA E:PHE209 4.4 16.8 1.0 CG E:PHE209 4.5 19.0 1.0 O E:PHE209 4.7 22.2 1.0 O E:THR208 4.8 24.2 1.0 CB E:PHE209 4.8 17.6 1.0

Sodium binding site 4 out of 4 in the 6218 Tcr in Complex with H2-Db Pa 224


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 6218 Tcr in Complex with H2-Db Pa 224 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:40.7 occ:1.00 CE E:MET27 2.2 30.8 1.0 SD E:MET2 2.6 43.7 1.0 SD E:MET27 2.7 35.0 1.0 CG E:MET27 2.8 31.5 1.0 CA E:MET2 2.9 35.5 1.0 CB E:MET2 3.1 37.4 1.0 CE1 E:HIS29 3.2 20.7 1.0 CG E:MET2 3.4 40.3 1.0 C E:MET2 3.5 35.7 1.0 N E:LYS3 3.5 28.6 1.0 NE2 E:HIS29 3.7 21.5 1.0 CB E:MET27 3.9 27.4 1.0 N E:MET2 4.1 37.4 1.0 O E:ASP1 4.1 43.4 1.0 ND1 E:HIS29 4.1 20.8 1.0 CD2 E:TYR113 4.2 22.1 1.0 CE E:MET2 4.3 41.1 1.0 CG E:TYR113 4.3 20.6 1.0 CE2 E:TYR113 4.5 23.4 1.0 C E:ASP1 4.5 44.2 1.0 O E:MET2 4.6 36.0 1.0 CD1 E:TYR113 4.7 24.5 1.0 OG E:SER106 4.8 16.9 1.0 CA E:LYS3 4.8 27.6 1.0 CD2 E:HIS29 4.8 21.5 1.0 CZ E:TYR113 4.8 33.1 1.0 O E:LYS3 4.8 24.2 1.0 CB E:TYR113 4.9 16.3 1.0 CE1 E:TYR113 4.9 26.2 1.0 C E:LYS3 4.9 26.1 1.0 CG E:HIS29 5.0 18.8 1.0

C.Szeto, P.Zareie, R.C.Wirasinha, J.B.Zhang, A.T.Nguyen, A.Riboldi-Tunnicliffe, N.L.La Gruta, S.Gras, S.R.Daley. Covalent Tcr-Peptide-Mhc Interactions Induce T Cell Activation and Redirect T Cell Fate in the Thymus. Nat Commun V. 13 4951 2022.
ISSN: ESSN 2041-1723
PubMed: 35999236
DOI: 10.1038/S41467-022-32692-4