Sodium in PDB 7rtr: Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01

The structure of Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01, PDB code: 7rtr 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)	33.42 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	225.356, 49.622, 91.725, 90, 91.83, 90
R / Rfree (%)	19.1 / 23.5

The binding sites of Sodium atom in the Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01 (pdb code 7rtr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01, PDB code: 7rtr:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:48.9 occ:1.00 O C:ARG5 2.5 35.9 1.0 NE2 A:HIS70 3.1 38.3 1.0 OE1 C:GLN3 3.1 46.3 1.0 NH1 A:ARG97 3.3 39.0 1.0 NH2 A:ARG97 3.5 30.8 1.0 CG C:GLN3 3.5 35.2 1.0 CD C:GLN3 3.6 48.3 1.0 CB C:GLN3 3.6 30.1 1.0 C C:ARG5 3.6 34.9 1.0 CE1 A:HIS70 3.7 38.1 1.0 O C:GLN3 3.8 31.5 1.0 CZ A:ARG97 3.8 42.9 1.0 CA C:THR6 3.8 30.1 1.0 CE2 A:TYR99 3.9 32.4 1.0 CG2 C:THR6 3.9 35.5 1.0 CD2 A:HIS70 3.9 37.8 1.0 OH A:TYR99 4.0 38.9 1.0 N C:THR6 4.2 31.2 1.0 CZ A:TYR99 4.3 37.9 1.0 C C:GLN3 4.3 31.6 1.0 CB C:THR6 4.4 37.3 1.0 O C:HOH101 4.4 38.3 1.0 CA C:GLN3 4.5 29.6 1.0 ND1 A:HIS70 4.6 38.0 1.0 NE2 C:GLN3 4.6 33.7 1.0 CE2 C:PHE7 4.6 31.1 1.0 CG A:HIS70 4.7 35.0 1.0 CD2 A:TYR99 4.8 32.2 1.0 N C:ARG5 4.8 28.6 1.0 CA C:ARG5 4.8 28.2 1.0 N C:GLN3 4.9 30.5 1.0 C C:THR6 5.0 32.1 1.0 CD2 C:PHE7 5.0 28.1 1.0

Sodium binding site 2 out of 4 in the Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:53.4 occ:1.00 OE1 A:GLU166 3.8 50.0 1.0 CE2 A:TRP167 4.3 31.4 1.0 NE1 A:TRP167 4.3 30.6 1.0 CB A:GLU166 4.5 34.5 1.0 CZ2 A:TRP167 4.5 30.5 1.0 NH1 A:ARG170 4.6 64.5 1.0 O A:GLU166 4.8 36.9 1.0 CD1 A:TRP167 4.8 31.6 1.0 CD A:GLU166 4.8 63.4 1.0 CD2 A:TRP167 4.9 28.5 1.0 C A:GLU166 5.0 36.1 1.0

Sodium binding site 3 out of 4 in the Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:46.8 occ:1.00 O D:GLU15 3.7 44.8 1.0 C D:GLY16 3.9 36.4 1.0 N D:ALA17 3.9 30.1 1.0 O D:GLY16 4.1 37.8 1.0 CA D:GLY16 4.2 32.7 1.0 CA D:ALA17 4.4 29.1 1.0 CB D:ALA17 4.5 28.9 1.0 C D:GLU15 4.6 41.4 1.0 N D:GLY16 4.9 33.6 1.0

Sodium binding site 4 out of 4 in the Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ylq-SG3 Tcr in Complex with Sars-Cov-2 Spike-Derived Peptide S269-277 (Ylqprtfll) Presented By Hla-A*02:01 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:57.8 occ:1.00 CA D:GLY64 3.7 35.4 1.0 O D:GLY64 3.7 42.5 1.0 C D:GLY64 3.8 41.7 1.0 N D:GLY64 3.9 35.5 1.0 O D:LEU80 4.1 30.3 1.0 OD1 D:ASP65 4.2 57.6 1.0 N D:ASP65 4.5 38.8 1.0 CG D:ASP65 4.5 57.1 1.0 OD2 D:ASP65 4.6 65.2 1.0 CB D:GLN79 4.7 33.0 1.0 NE2 D:GLN79 4.7 52.1 1.0 N D:LEU80 4.8 30.0 1.0 C D:LEU80 4.8 31.7 1.0

C.Szeto, A.T.Nguyen, C.A.Lobos, D.S.M.Chatzileontiadou, D.Jayasinghe, E.J.Grant, A.Riboldi-Tunnicliffe, C.Smith, S.Gras. Molecular Basis of A Dominant Sars-Cov-2 Spike-Derived Epitope Presented By Hla-A*02:01 Recognised By A Public Tcr Cells V. 10 2021.
ISSN: ESSN 2073-4409
DOI: 10.3390/CELLS10102646