Electron-nuclear double resonance (ENDOR) is a method that probes the local structure of paramagnetic centers via their hyperfine interactions with nearby magnetic nuclei. Here we describe the use of this technique to structurally characterize the ATPase active site of the RNA helicase DbpA, where Mg2+-ATP binds. This is achieved by substituting the EPR (electron paramagnetic resonance) silent Mg2+ ion with paramagnetic, EPR active, Mn2+ ion. 31P ENDOR provides the interaction of the Mn2+ with the nucleotide (ADP, ATP and its analogs) through the phosphates. The ENDOR spectra clearly distinguish between ATP- and ADP-binding modes. In addition, by preparing 13C-enriched DbpA, 13C ENDOR is used to probe the interaction of the Mn2+ with protein residues. This combination allows tracking structural changes in the Mn2+ coordination shell, in the ATPase site, in different states of the protein, namely with and without RNA and with different ATP analogs. Here, a detailed description of sample preparation and the ENDOR measurement methodology is provided, focusing on measurements at W-band (95 GHz) where sensitivity is high and spectral interpretations are relatively simple.