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

The structure of Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984), PDB code: 8rhq 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)	42.75 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.492, 85.492, 312.028, 90, 90, 120
R / Rfree (%)	19.8 / 24.4

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

Chlorine	(Cl)	3 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) (pdb code 8rhq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984), PDB code: 8rhq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, 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 Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:33.6 occ:1.00 O B:LEU87 2.2 24.7 1.0 O B:HIS84 2.4 25.4 1.0 O B:HOH207 2.4 32.4 1.0 OD1 B:ASN83 2.4 24.0 1.0 O B:HOH228 2.6 35.7 1.0 CG B:ASN83 3.2 32.2 1.0 C B:HIS84 3.3 24.4 1.0 C B:LEU87 3.4 26.5 1.0 ND2 B:ASN83 3.5 34.8 1.0 N B:HIS84 3.8 21.3 1.0 O B:HOH231 3.8 36.1 1.0 N B:LEU87 4.1 24.4 1.0 CA B:VAL85 4.1 20.6 1.0 N B:VAL85 4.1 22.0 1.0 CA B:LEU87 4.1 31.1 1.0 CA B:HIS84 4.2 22.2 1.0 CB B:LEU87 4.3 18.8 1.0 O B:SER88 4.3 41.8 1.0 C B:VAL85 4.3 27.4 1.0 O B:VAL85 4.4 25.7 1.0 N B:SER88 4.5 37.0 1.0 CB B:ASN83 4.6 24.9 1.0 C B:SER88 4.6 35.6 1.0 CA B:SER88 4.7 34.0 0.1 CA B:SER88 4.7 33.9 0.8 C B:ASN83 4.7 26.7 1.0 CA B:ASN83 4.9 31.2 1.0 N B:THR86 5.0 25.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, 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 Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na404 b:17.2 occ:1.00 OD1 E:ASN86 2.4 17.1 1.0 O E:GLY83 2.5 14.7 1.0 C E:GLY83 3.4 11.7 1.0 CG E:ASN86 3.6 15.4 1.0 CA E:GLY83 3.7 11.0 1.0 O E:HOH607 4.0 16.7 1.0 CA E:ASN86 4.2 16.2 1.0 N E:ASN86 4.4 15.6 1.0 ND2 E:ASN86 4.5 19.4 1.0 CB E:ASN86 4.5 18.5 1.0 N E:TYR84 4.6 11.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, 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 3 of Crystal Structure of Hla-A*11:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na103 b:32.4 occ:1.00 O F:HIS84 2.4 32.4 1.0 OD1 F:ASN83 2.6 28.4 1.0 O F:HOH231 2.6 29.3 1.0 O F:LEU87 2.7 31.2 1.0 CG F:ASN83 3.2 36.6 1.0 C F:HIS84 3.3 35.7 1.0 ND2 F:ASN83 3.3 30.3 1.0 N F:HIS84 3.8 25.9 1.0 C F:LEU87 3.8 30.3 1.0 N F:VAL85 4.1 32.1 1.0 CA F:VAL85 4.2 29.5 1.0 CA F:HIS84 4.2 30.1 1.0 O F:HOH233 4.2 37.0 1.0 N F:LEU87 4.3 24.3 1.0 CB F:LEU87 4.4 31.3 1.0 CA F:LEU87 4.4 36.6 1.0 C F:VAL85 4.5 28.0 1.0 CB F:ASN83 4.5 26.9 1.0 O F:VAL85 4.6 39.9 1.0 C F:ASN83 4.7 27.8 1.0 CA F:ASN83 4.9 30.2 1.0 N F:SER88 4.9 40.4 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