Sodium in PDB 7m8t: Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378)

The structure of Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378), PDB code: 7m8t was solved by S.Gras, A.T.Nguyen, C.Szeto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.41 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.873, 38.451, 110.059, 90, 94.63, 90
R / Rfree (%)	18.8 / 21.9

The structure of Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378) also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378) (pdb code 7m8t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378), PDB code: 7m8t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378)


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 Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:40.2 occ:1.00 N A:ASP223 3.0 16.0 1.0 CG A:ASP223 3.6 25.6 1.0 CA A:GLU222 3.7 15.9 1.0 CB A:ASP223 3.7 18.3 1.0 C A:GLU222 3.8 15.7 1.0 OD1 A:ASP223 3.9 26.6 1.0 OD2 A:ASP223 3.9 30.5 1.0 O A:HOH596 3.9 27.0 1.0 CA A:ASP223 3.9 16.0 1.0 O A:GLY221 4.3 20.6 1.0 CB A:GLU222 4.4 17.3 1.0 N A:GLU222 4.8 16.1 1.0 O A:ASP223 4.9 17.6 1.0 C A:ASP223 5.0 16.1 1.0 O A:GLU222 5.0 15.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378)


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 Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:48.1 occ:1.00 N B:THR4 3.4 20.9 1.0 OG1 B:THR4 3.6 23.8 0.4 CG2 B:THR4 3.8 25.0 0.6 CB B:THR4 3.9 22.8 0.4 CA B:ARG3 3.9 23.8 1.0 CB B:THR4 4.2 24.1 0.6 C B:ARG3 4.2 21.6 1.0 CA B:THR4 4.3 21.4 1.0 CB B:ARG3 4.4 23.6 1.0 O B:GLN2 4.6 31.5 1.0 O B:THR4 4.7 21.4 1.0 CG B:ARG3 5.0 28.5 1.0

A.T.Nguyen, C.Szeto, D.Jayasinghe, C.A.Lobos, H.Halim, D.S.M.Chatzileontiadou, E.J.Grant, S.Gras. Sars-Cov-2 Spike-Derived Peptides Presented By Hla Molecules Biophysica V. 1 2021.
DOI: 10.3390/BIOPHYSICA1020015