Sodium in PDB 8rcv: Crystal Structure of Hla B*13:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984)

The structure of Crystal Structure of Hla B*13:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984), PDB code: 8rcv 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)	41.37 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.061, 82.734, 109.52, 90, 90, 90
R / Rfree (%)	17.9 / 20.1

The binding sites of Sodium atom in the Crystal Structure of Hla B*13:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984) (pdb code 8rcv). 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 B*13:01 in Complex with Svlndifsrl, An 10-Mer Epitope From Sars-Cov-2 Spike (S975-984), PDB code: 8rcv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hla B*13:01 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 B*13:01 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 A:Na402 b:50.1 occ:1.00 OD2 A:ASP119 3.9 17.9 1.0 CG A:ASP119 4.0 15.9 1.0 CB A:ASP119 4.2 16.6 1.0 N B:ILE1 4.4 43.2 1.0 O B:HOH222 4.4 27.1 1.0 O A:HOH535 4.5 21.4 1.0 O A:HOH614 4.5 20.9 1.0 OD1 A:ASP119 4.6 15.2 1.0 O B:ILE1 4.8 42.9 1.0 ND1 A:HIS93 4.8 16.2 1.0 CE1 A:HIS93 4.9 15.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hla B*13:01 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 B*13:01 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:Na102 b:26.6 occ:1.00 O B:HOH263 2.3 28.6 1.0 O B:HOH267 2.3 29.7 1.0 O B:LEU87 2.5 26.4 1.0 O B:HIS84 2.5 21.3 1.0 OD1 B:ASN83 2.6 21.1 1.0 O B:HOH261 2.6 30.6 1.0 CG B:ASN83 3.4 25.0 1.0 C B:HIS84 3.5 18.7 1.0 C B:LEU87 3.6 22.4 1.0 ND2 B:ASN83 3.7 26.8 1.0 N B:HIS84 4.0 17.2 1.0 N B:LEU87 4.1 19.7 1.0 CA B:VAL85 4.2 19.1 1.0 N B:VAL85 4.2 17.5 1.0 CA B:LEU87 4.3 22.4 1.0 CB B:LEU87 4.3 24.8 1.0 C B:VAL85 4.4 27.5 1.0 CA B:HIS84 4.4 17.3 1.0 O B:VAL85 4.4 23.8 1.0 O B:HOH268 4.5 28.4 1.0 O B:SER88 4.5 32.3 1.0 CB B:ASN83 4.7 23.0 1.0 C B:SER88 4.7 33.5 1.0 N B:SER88 4.7 25.6 1.0 C B:ASN83 4.9 17.8 1.0 CA B:SER88 5.0 26.6 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