NMR characterization and ligand binding site of the stem–loop 2 motif from the Delta variant of SARS-CoV-2

(A) Crystal structure of s2m SCoV-1 and secondary structures of s2m SCoV-1 (B), SCoV-2 (C), and SCoV-2 Delta (D). The crystal structure for SCoV-1 (Robertson et al. 2005) was taken from the pdb: 1XJR. Nucleotides that differ between SCoV-1 and SCoV-2 are highlighted in red and the Delta mutation is highlighted in magenta. The new base pair that can be formed in Delta is shown in a gray box. The numbering of nucleotides corresponds to the position in the genome −29,000. The nucleotide notation for SCoV-1 is adjusted to match the notation in SCoV-2. (E) Sequence alignment of s2m SCoV-1, SCoV-2, and SCoV-2 Delta. Nucleotides that differ compared to s2m SCoV-2 are highlighted in red or magenta with a gray box.