Figure. 2. Non-catalytic interaction between the 5′-CC dinucleotide and sA3G*.

a Interactions between dinucleotide and sA3G*-CTD. The Watson-Crick faces of both cytosines (C1 and C2) position towards loop-7 and the catalytic Zn²⁺ ion. sA3G* is colored yellow and shows the side chains as sticks. Atoms in the dinucleotide are colored blue, navy, red and orange for C, N, O and P respectively. Water molecules are shown as red spheres, and Zn²⁺ is shown as a purple colored sphere. Gray dotted lines indicate hydrogen bonding. b Superimposition of the sA3G*:dinucleotide structure (this study, dinucleotide is colored blue) with the A3G-CTD2:ssDNA structure (PDB ID: 6BUX, ssDNA is colored pink) comparing positions of nucleotides in the two structures. The double arrow-headed line points to the backbone phosphorous atoms of C2 of the dinucleotide and C⁻¹ of the A3G-CTD2:ssDNA structure. c Superimposition of the sA3G* structure (this study, sA3G* is colored yellow) with the A3G-CTD2 structure (PDB ID: 6BUX, A3G-CTD2* is colored light purple) highlighting side-chain conformational differences of key amino acid residues for ssDNA substrate binding. DNAs are not shown. d Superimposition of the sA3G*-dinucleotide structure (this study, dinucleotide is colored blue) with the adenine bound A3G-CTD structure (PDB ID: 6BWY, adenine is colored magenta) showing overlap of the adenine base with the C1 base of the dinucleotide. Dotted lines indicate hydrogen bonds between the adenine amino group and two mainchain carbonyls; I314 and P210 of A3G-CTD (gray colored sticks). e Summary of the interactions between sA3G* and the dinucleotide.