FIGURE 3.
Displacement of H89 during aa-tRNA elbow accommodation. (A) Structure of A/T conformation with aa-tRNA (yellow), p-tRNA (red), mRNA (green), H89 (purple), and stem–loop of H89 (violet) shown. The distance between the stem–loop of H89 and the A-site codon (H89-codon), is indicated by the pink bar. The green bar indicates RElbow (as defined in Fig. 1B). (B) Probability distribution of H89-codon versus RElbow, calculated from 312 unrestrained structure-based simulations. Only structures in which the arm is not accommodated (RArm > 12 Å) are included in the distribution. The gray line is the average H89-codon distance as a function of RElbow. Note: X-axis is inverted for visual ease. As the aa-tRNA elbow accommodates (i.e., RElbow decreases) H89-codon increases when the aa-tRNA contacts the stem–loop of H89 (RElbow ∼ 49 Å) and then reduces after the aa-tRNA elbow has accommodated.