Figure 2

(A) Hydrogen bonding and steric interactions between the first two nucleotides of the UAA stop codon with the reading head of RF1 in T. thermophilus(from PDB entry 3D5A [7]). (B) Molecular model of the reading head conformation in the mtRF1. Residues at positions interacting with the stop codon in panel A are shown. (C) Stabilizing interaction between A-1493 of the ribosomal decoding centre (shown in blue) and the switch loop (shown in green) of release factor RF1 in T. thermophilus (from PDB entry 3MR8 [8]). (D) Stabilizing interaction between the arginine of the RT-insert and the switch loop of mtRF1 when the A-site is empty. Coordinates of the ribosomal decoding centre (shown in blue) are taken from PDB entry 1IBM [11]. All numbering according to the T. thermophilus RF1 sequence.