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. 2006 Jul 19;34(12):3599–3608. doi: 10.1093/nar/gkl494

Figure 5.

Figure 5

The aminoglycoside analogue 1 binds to the upper stem major groove. (A) View of the best energy structure of the family of Figure 4. The aminoglycoside analogue 1 (color coded by atom: dark gray, red and blue sticks) is placed in the major groove of the upper stem of the HIV-2 TAR-RNA. A22 and U40, depicted in orange, clearly show that the hydrogen bonds between 22 and 40 are disrupted and that A22 tilts away from the major groove to accommodate the ligand. Besides A22 and G26, U23 (magenta), U25 (turquoise) and A35 (pink) have direct contacts with the aminoglycoside analogue. The positively charged amino group of the ligand sugar-1 interacts with the π-orbital of the A35 base, the amino group of sugar-3 interacts electrostatically with the major groove edge of G28 (dashed yellow line), while the amino group of sugar-5 contacts the phosphate of A22 (dashed yellow line). G34 (yellow sticks) stacks on the top of G36. The backbone of the loop is shown as yellow lines. A similar intermolecular interaction pattern is observed also for the other structures of the ensemble. (B) Same as in (A) after 90° rotation around the vertical axis.