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. 2025 Aug 14;122(33):e2506491122. doi: 10.1073/pnas.2506491122

Fig. 3.

Fig. 3.

Architecture of the binding pocket. (A) An overall view of the binding pocket structure. (B and C) The nucleobase of ATP stacks with T8·A28 base pair and G9. (D) N1 of ATP forms a hydrogen bond with G14 H21/H22, and HO2′ of ATP forms a hydrogen bond with G30 O6. The aptamer and ATP are shown in stick mode. (E) ITC analysis of ATP binding of 1301b_v1 mutants. “#” means no binding. Data represent mean ± SD from three independent ITC measurements. The original ITC data are shown in SI Appendix, Figs. S13–S15 and S17. (F) The binding pocket structure of the classic DNA aptamer in complex with two molecules of AMP (PDB ID: 1AW4) (21). (G and H) The binding pocket structures of the 36-nt RNA aptamer–AMP complex (PDB ID: 1RAW) (22) and the 40-nt RNA aptamer–AMP complex (PDB ID: 1AM0) (23).