Figure 2.

Conservation of the guide RNA 5′-nucleotide-binding pocket. (A) Electrostatic potential mapped onto the molecular surface of the Nc QDE-2 MID domain, with the two bound sulphates shown as yellow sticks. Potentials are contoured from −10 (red) to +10 kT/e (blue). The 5′-RNA nucleotide from the superposition with the Af MID domain in complex with a guide RNA (Fig 1B,C) is shown as grey sticks. (B) Close-up of the RNA 5′-end nucleotide-binding site. The superimposed 5′-uridine from the Af complex structure is shown as sticks, together with the two sulphates and important side chains from the Nc QDE-2 structure. The uridine base stacks on the aromatic Tyr 595 ring, whereas the 5′-phosphate superimposes with sulphate I. Red: oxygen; blue: nitrogen; yellow: sulphur; violet: phosphorus. Af, Archaeoglobus fulgidus; MID, middle; Nc, Neurospora crassa; QDE-2, quelling deficient 2.