Fig. 6. Three-dimensional model of the complex between subdomain ID, domain V and the ligated exons. (A) Coloring by domains: dark gray, exons; green, basal section of ID [ID⁽ⁱ⁾–ID^(iv)]; blue, ID3; yellow, ID2 stem and basal loop; orange, IB; magenta, domain V. Numbering is according to Figure 3A. The EBS3–IBS3(+1) and δ–δ′ base pairs are shown in red. (B) Coloring (except for domain V and the exons) is according to the extent of protection from hydroxyl radical cleavage in the presence of magnesium (values from Figure 7B; values could not be obtained for positions 202–207, shown in off-white, see legend to Figure 7C). Nucleotides shown in domain V (pink) are those whose reactivity changes upon binding of the 5′ exon. Figure prepared with Ribbons (Carson, 1991).