We describe in detail the use of 35 GHz Mims pulsed N-15 and H-1,H-2 electron-nuclear double resonance (ENDOR) spectroscopy to study the binding of substrates and inhibitors to nitric oxide synthase (NOS). We show that reliable distance estimates, and limited orientation information, can be derived from a small set of data taken near the peak of the absorption mode EPR signal, while more precise orientations require a more extensive data set. The ENDOR approach is then applied to the binding of isoform-selective and non-selective nitroarginine inhibitors. Recently, we reported a family of Nw-nitroarginine-containing dipeptide amides as highly selective inhibitors of nNOS (Huang, H. et al. J. Med. Chem. 1999, 42, 3147-3153). Two of the most potent analogues were the retro-inverso-dipeptide amides L-Arg(NO2)-L-Lys-NH2 (LL) and D-Lys-D-Arg(NO2)-NH2 (DD). To rationalize the common selectivities of LL and DD, it was proposed that in both cases the nitroarginine group binds at the heme binding site, therefore requiring one of these molecules to undergo a 180 degrees flip to accommodate such an interaction. The present studies confirm that the dipeptides indeed bind to holo-nNOS quite similarly from the point of view of the nitroguanidine functionality, supporting the earlier interpretation. The data further suggest that a substantial fraction of the DD epimer is distributed among other binding geometries.