To understand the nature of the thyroid hormone binding site, we characterized the binding of 3,3',5-triiodo-L-thyronine (T3) and its analogues to eight naturally occurring mutated human beta1 thyroid hormone receptors (h-TRbeta1). The mutant receptors were derived from patients with the syndrome of generalized thyroid hormone resistance, and each has a point mutation in the hormone binding domain (KT, R338W; TP, L450H; IR, D322H; NN, G347E; AH, P453H; OK, M442V; RL, F459C; and ED, A317T). Compared to the wild-type h-TRbeta1, binding of T3 was reduced by as much as 97% for the mutants. The order of binding affinity of wild-type h-TRbeta1 to the analogues is T3 > D-T3 > L-thyroxine > 3,5-diiodo-L-thyronine > 3,3',5'-triiodo-L-thyronine. The mutant receptors showed essentially the same order of reduced affinities for the analogues, but the amounts of the reductions varied in each case. These results suggest specific local interactions (interplay) of analogues with the mutated residues in the receptors. On the basis of these data and a putative structure of the hormone binding domain as an eight-stranded alpha/beta barrel, we propose the location of the hormone in the binding site of h-TRbeta1. Ionic bonds anchor the hormone's alanine side chain to loop 4 of the 8-fold alpha/beta barrel. The phenyl ring lies across the amino-terminal face of the domain with the phenoxy ring pointing downward into the barrel interacting with beta-strand 8 on the opposite side. Loops 1 and 7, which are located on the same face as the DNA binding domain, fold over the top of the barrel toward the bound hormone. The T3-induced conformational changes observed by us and others may be partly mediated by loops 1 and 7. The present model should provide a basis for further studies to understand the T3-dependent transcriptional activity of h-TRbeta1.