Cadmium in PDB 8rbv: Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01

The structure of Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01, PDB code: 8rbv 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.821, 78.177, 110.911, 90, 90, 90
R / Rfree (%)	18 / 21.1

The binding sites of Cadmium atom in the Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01 (pdb code 8rbv). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01, PDB code: 8rbv:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:26.1 occ:1.00 ND1 A:HIS191 2.4 25.5 1.0 O A:HIS191 2.5 20.7 1.0 C A:HIS191 3.2 20.5 1.0 CG A:HIS191 3.3 26.6 1.0 CE1 A:HIS191 3.4 31.6 1.0 CB A:HIS191 3.5 23.5 1.0 CA A:HIS191 3.9 20.8 1.0 N A:HIS192 4.0 20.1 1.0 CA A:HIS192 4.2 19.2 1.0 O A:HOH598 4.3 25.1 1.0 NE2 A:HIS191 4.5 25.1 1.0 CD2 A:HIS191 4.5 25.9 1.0 N A:HIS191 4.6 23.0 1.0 N A:ALA193 4.6 23.1 1.0 C A:HIS192 4.9 25.5 1.0

Cadmium binding site 2 out of 2 in the Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Sars-Cov-2 Spike-Derived Peptide S976-984 S982A Mutant (Vlndilarl) Presented By Hla-A*02:01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:47.3 occ:1.00 NE2 A:HIS145 2.6 31.6 1.0 CD2 A:HIS145 3.4 38.5 1.0 CE1 A:HIS145 3.7 38.1 1.0 NE2 A:GLN141 4.2 35.9 1.0 CG A:GLN141 4.3 28.7 1.0 CG A:HIS145 4.6 32.3 1.0 ND1 A:HIS145 4.7 34.2 1.0 CD A:GLN141 4.7 32.0 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