Figure 1. Cloverleaf folding of transfer RNA (tRNA) with location of known identity nucleotides. The standard cloverleaf structure and conventional numbering system are used. Constant nucleotides are explicitly indicated (T and are modified residues: ribothymidine and pseudouridine). The · symbol indicates Watson–Crick base pairings, including G·U pairs; thin black lines indicate other base pairings. The inset represents the L-shaped structure of tRNA and highlights its different domains. To designate identity positions for a given amino acid, the single-letter code for amino acids is used. The figure emphasizes the clustering of the strongest identity elements in three domains of the tRNA molecule: the two distal extremities and the core region. Notice that not all of the nucleotides at these positions are used for a given identity (e.g. only G₃·U₇₀ for alanine identity; only U₃₅ and A₇₃ for tyrosine identity). The figure makes a distinction between identities of tRNAs recognized by class I and class II synthetases. ^aVariable region (e.g. long extra arm of tRNA^Ser, nucleotides 44–48 for tRNA^Phe); ^bLevitt pair 15–48 of tRNA^Cys; ^cvariable pocket (nucleotide 20 for tRNA^Ala, tRNA^Arg, tRNA^Leu and tRNA^Phe). Characterized individual modified nucleosides that act as identity determinants in tRNA anticodon loops are shown in the inset (k²C, lysidine; s²U, 2-thiouridine; mnm⁵s²U, 5-methylaminomethyl-2-thiouridine; Q, queuosine; I, inosine; , pseudouridine; m¹G, 1-methylguanosine; t⁶A, N-6-threonylcarbamoyladenosine and yW, wybutosine).

Figure 2. Conformations of the ATP molecules interacting with class I and class II synthetases. The ATP conformations are those found in the GlnRS–tRNA^Gln–ATP (left side) and AspRS–tRNA^Asp–ATP (right side) complexes. In class I aaRSs, the ATP molecule exhibits an extended conformation reminiscent of that found in other enzymes containing a Rossmann fold. In class II aaRSs, the ATP adopts a bent conformation with the -phosphate folded back over the adenine base. The figure displays the ATP molecule in two orientations with the adenine ring facing the reader (top) or rotated by 90° (bottom).

Figure 3. Different binding modes of the ATP and tRNA molecules observed in the class I GlnRS–tRNA^Gln–ATP complex and the class II AspRS–tRNA^Asp–ATP complex. The upper part of the figure shows the ATP positions relative to the tRNA acceptor arms. The lower part of the figure shows the different binding approaches of the tRNA molecule.