Heme binds selectively to the 3'-terminal G-quartet of all parallel G-quadruplex DNAs to form stable heme-DNA complexes. Interestingly, the heme-DNA complexes exhibit various spectroscopic and functional properties similar to those of hemoproteins. Since the nature of the axial ligands is crucial in determining the physicochemical properties of heme, identification and characterization of the axial ligands in a heme-DNA complex are essential to elucidate the structure-function relationship in the complex. NMR studies of a complex possessing a low-spin ferric heme with a water molecule (H2O) and cyanide ion (CN-) as the axial ligands allowed detailed characterization of the physicochemical nature of the axial H2O ligand. We found that the in-plane asymmetry of the heme electronic structure of the complex is not largely affected by the axial H2O coordination, indicating that the H2O confined in the hydrophobic interface between the heme and G-quartet planes of the complex rotates about the coordination bond with respect to the heme. The effect of the hydrogen(H)/deuterium(D) isotope replacement of the axial H2O on the heme electronic structure was manifested in the isotope shifts of paramagnetically shifted heme methyl proton signals of the complex in such a manner that three resolved peaks associated with axial H2O, HDO, and D2O were observed for each of the heme methyl proton signals. These findings provide not only the basis for an understanding of the nature of the unique axial H2O but also an insight into the molecular mechanism responsible for the control of the heme reactivity in the heme-DNA complex.