Modeling steps to rebuild the A-site. (A) First, nucleotide 530 (purple) of loop 530 in the rRNA and nucleotides 34 (green), 35 (marine), and 36 (orange) of the anticodon loop are sampled using the MC-Sym computer program. An adjacency relationship (adjacent) is used to position nucleotide 36 with respect to 37 and so on down to nucleotide 34 in the tRNA. A stacking relationship (stack) positions 530 with respect to 518. (B) Second, nucleotides of the messenger RNA (1, red; 2, green; 3, marine) and the two adenosines 1492 (orange) and 1493 (purple) in the rRNA are sampled in the context of a given conformation chosen from step 1. Here, nucleotides in the mRNA are positioned using a pairing relationship (pair) with respect to their paired partner in the tRNA (anticodon 36 positions mRNA 1, 35 positions 2, and 34 positions 3). A1493 of rRNA pairs with 36 of tRNA, while A1492 of rRNA pairs with mRNA residue 2.
