The active site of the oxygenase component of naphthalene 1,2-dioxygenase (NDO) contains a Rieske Fe-S cluster and a mononuclear non-heme iron, which are contributed by different α-subunits in the (αβ)3 structure. The enzyme catalyzes cis-dihydroxylation of aromatic substrates in addition to numerous other adventitious oxidation reactions. High-resolution Mims 2H-ENDOR spectra have been recorded for the NO-ferrous center of NDO bound with d8-naphthalene and d2-naphthalene; spectra were collected for the enzyme with the Rieske diiron center both in its oxidized and in its reduced states. A sharp quartet ENDOR pattern from a nearby deuteron of substrate was detected for each substrate. Examination of the sample prepared with 1,4-dideutero-naphthalene shows that the signal arises from D1. The ENDOR data place D1 at a distance of ca. 4.4 Å from the mononuclear Fe and with the Fe-D vector being roughly along the Fe-N(O) direction. Because reduction of the Rieske cluster is required for O2 binding and subsequent catalysis, the effect of its oxidation state on substrate binding was examined. The spectra from the NDO-naphthalene complex reveal two different binding conformations, which change in relative population when the oxidation state of the Rieske cluster is changed. This shift, and the conformational coupling it implies, may hold the key to both oxygen gating and oxygen reactivity for Rieske aromatic dioxygenases.