Chlorine in PDB 8rbu: Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984)

The structure of Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984), PDB code: 8rbu was solved by Y.M.Ahn, J.C.Maddumage, C.Szeto, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.67 / 2.70
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.992, 86.992, 107.183, 90, 90, 120
R / Rfree (%)	20.4 / 25.2

The structure of Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) (pdb code 8rbu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984), PDB code: 8rbu:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984)


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 Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:50.3 occ:1.00 NE A:ARG82 3.1 50.7 1.0 NH2 A:ARG82 3.4 60.2 1.0 CA A:GLY79 3.5 31.8 1.0 CG A:ARG17 3.6 58.0 1.0 N A:GLY79 3.6 28.6 1.0 CD A:ARG17 3.7 47.5 1.0 CZ A:ARG82 3.7 50.0 1.0 C A:LEU78 3.9 33.2 1.0 O A:LEU78 3.9 34.3 1.0 CB A:ARG17 3.9 53.6 1.0 CA A:ARG17 4.2 58.7 1.0 NE A:ARG17 4.2 51.9 1.0 CD A:ARG82 4.2 40.8 1.0 O A:HOH501 4.2 48.0 1.0 CB A:SER13 4.3 39.0 1.0 CB A:LEU78 4.4 27.8 1.0 CB A:ARG82 4.5 30.9 1.0 CZ A:ARG17 4.7 46.0 1.0 NH1 A:ARG17 4.7 45.0 1.0 OG A:SER13 4.8 43.0 1.0 CA A:LEU78 4.8 28.2 1.0 C A:GLY79 4.8 33.4 1.0 O A:HOH513 4.9 52.2 1.0 CG A:ARG82 4.9 40.3 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984)


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 Hla-A*11:01 in Complex with Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl103 b:67.5 occ:1.00 N B:VAL9 3.4 50.1 1.0 O B:VAL9 3.6 49.0 1.0 CA B:GLN8 3.7 37.5 1.0 C B:GLN8 4.1 41.0 1.0 CB B:GLN8 4.2 37.3 1.0 CA B:VAL9 4.3 44.4 1.0 C B:VAL9 4.3 42.6 1.0 CG B:GLN8 4.4 36.6 1.0 O B:ILE7 4.4 35.4 1.0 OE1 B:GLN8 4.6 46.4 1.0 CG1 B:VAL93 4.7 31.0 1.0 CB B:VAL9 4.7 43.1 1.0 O B:MET99 4.8 42.7 1.0 N B:GLN8 4.9 36.5 1.0 CB B:MET99 4.9 40.7 1.0 NH1 A:ARG234 5.0 40.7 1.0 CD B:GLN8 5.0 47.2 1.0

Y.M.Ahn, J.C.Maddumage, E.J.Grant, D.S.Chatzileontiadou, W.G.Perera, B.M.Baker, C.Szeto, S.Gras. The Impact of Sars-Cov-2 Spike Mutation on Peptide Presentation Is Hla Allomorph-Specific Curr Res Struct Biol 2024.
ISSN: ESSN 2665-928X
DOI: 10.1016/J.CRSTBI.2024.100148