Sodium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 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 Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984)


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 Svlndilarl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:56.9 occ:1.00 CE A:LYS186 3.2 62.4 1.0 NZ A:LYS186 3.5 61.9 1.0 ND1 B:HIS13 3.9 43.0 1.0 O A:HOH512 4.2 36.9 1.0 CB A:LEU206 4.4 31.4 1.0 CD B:PRO14 4.5 50.0 1.0 CD A:LYS186 4.6 61.2 1.0 CE1 B:HIS13 4.6 37.0 1.0 O B:ARG12 4.7 46.7 1.0 CG B:HIS13 4.9 46.6 1.0 CD1 A:LEU206 4.9 36.9 1.0 CA B:HIS13 4.9 47.2 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na104 b:42.4 occ:1.00 OE2 B:GLU36 3.8 76.8 1.0 CG B:GLU36 3.9 60.0 1.0 CD B:GLU36 3.9 71.2 1.0 O B:ASN83 4.0 39.3 1.0 CA B:HIS84 4.3 31.5 1.0 O B:ASP34 4.4 41.0 1.0 C B:ASN83 4.4 41.0 1.0 ND2 B:ASN83 4.5 54.8 1.0 C B:HIS84 4.5 38.7 1.0 OE1 B:GLU36 4.6 69.6 1.0 N B:VAL85 4.6 38.0 1.0 N B:GLU36 4.6 44.5 1.0 N B:HIS84 4.6 41.1 1.0 CA B:ILE35 4.6 34.2 1.0 C B:ASP34 4.7 36.6 1.0 CB B:GLU36 4.8 39.8 1.0 N B:ILE35 4.8 38.9 1.0 CG B:ASN83 4.8 44.4 1.0 C B:ILE35 4.9 40.6 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