Fig. 3.

Stem I₅₇ crystal structure. (A) Secondary structure of the stem I₅₇ crystallization construct with tertiary contacts drawn by using the Leontis–Westhof notation (43), with the AG bulge (magenta) and distal loop (green) highlighted. (B and C) Orthogonal views of the stem I₅₇ crystal structure shown as a cartoon, colored as in A. (D) Stereo image of the AG bulge–distal loop interaction. (E) The apical base triple, highlighted in sticks, colored as in B and C. Oxygen, nitrogen, and phosphorus are shown in red, blue, and orange, respectively. Hydrogen bonds are shown as dashed lines. Stem I₅₇ is in the same orientation as in C. (F) Superposition of the stem I apical loops (cyan) and the RNase P specificity domain (orange), which is in complex with tRNA (gray) [Protein Data Bank (PDB) ID 3Q1Q]. Structures are shown as ribbons with interacting bases highlighted in sticks. Hydrogen bonds in the stem I apical base triple are highlighted as dashed lines.