Fig. 5.

Nucleotide induced conformational changes in NS3 lead to differences in RNA binding. (a) Structural overlay of nucleotide-free NS3-rU8Br4 (colored according to Fig. 1) and NS3-rU8Br4/ADP•BeF₃ (gray). (b) Local conformational change in of motif V of D2. Motif V (residues 411–419) in the nucleotide-free structure (green helical coil and sticks) rearranges upon binding to ADP•BeF₃ (spheres), resulting in the repositioning of Thr 416. For clarity, only U5 of the RNA is shown (cyan sticks, nucleotide-free structure; gray sticks, nucleotide-bound structure). (c) Comparison of RNA binding to NS3 in the nucleotide-bound and nucleotide-free states. The nucleotide-bound structure (+Nuc, gray coil and sticks) and the nucleotide-free structure (−Nuc, green coils and cyan sticks) are overlaid. Thr 416, Trp 501 and RNA nucleotides are labeled accordingly.