Fig. 3: Structure of the fluorophore-binding core and the ligand TMR-DN.
From: Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST
a Crystal structure of the ligand TMR-DN intercalated into the fluorophore-binding core. The red mesh grid depicts the 2|Fo|–|Fc| electron density map of the ligand (contour level: sigma = 1.0). b Surface representation of semi-open binding pocket formed with the capping loop and the underneath A32•A50•A45 base triple in two views. c The fluorophore TMR is sandwiched below the G47 nucleobase and above nucleobases of A32 and A50. d G47 nucleobase forms hydrogen bonds with the G46 sugar ring and U49 nucleobase. e The O2´ of U49 forms two hydrogen bonds with N6 of A32 and O6 of G34, respectively. f Stick representation of the RhoBAST-bound TMR-DN ligand (RhoBAST not shown) in two views. The phenyl ring of TMR adopts an inclined orientation (~60°) to the tricyclic ring of xanthene, which is partially stacked with the quencher DN. g The DN quencher and the ortho-carboxylate group within the phenyl ring form one and two hydrogen bonds with the nucleobase of G47, respectively.
