Escherichia coli Ile-tRNA synthetase and tRNA-Ile have been cross-linked photochemically by the direct action of ultraviolet light. In addition, photo-induced joining of tRNA-Ile E. coli to Val-tRNA synthetase from yeast has also been achieved. This yeast enzyme is known to mischarge E. coli tRNA-Ile with valine. Regions on tRNA-Ile involved in cross-linking have been determined for both complexes. In each case, three distinct parts of the nucleic acid are found cross-linked. Two of these are the same in both complexes and involve the dihydrouridine stem and loop region. The third part is unique for each complex. It involves the 3' terminus in the cognate one and the 3' side of the anticodon in the non-cognate case. When the cross-linked regions are projected onto a model of the three-dimensional structure of tRNA, it is clear that these and other data are consistent with having each enzyme bound in a similar orientation across tRNA-Ile. The enzymes are viewed as spanning the distance from the anticodon to the 3' terminus and making extensive contact with the area in which the two helical branches of the L-shape tRNA structure come together.