Because of their presence in the nuclear fuel cycle, neptunium and uranium are two actinides of main interest in case of internal contamination. Complexation of U(VI) and Np(V) by the target protein calmodulin (CaM(WT)) was therefore studied herein. Both actinides have two axial oxygen atoms, which, charge aside, makes them very similar structurally wise. This work combines spectroscopy and theoretical density functional theory (DFT) calculations. Structural characterization was performed by extended X-ray absorption fine structure (EXAFS) at the L(III)-edge for each studied actinide. Models for the binding site of the protein were developed and then refined by using DFT to fit the obtained experimental EXAFS data. The effect of hydrolysis was also considered for both actinides (the uranyl experiment was performed at pH 3 and 6, while the neptunyl experiment was conducted at pH 7 and 9). The effect of the pH variation was apparent on the coordination sphere of the uranyl complexes, while the neptunyl complex characteristics remained stable under both studied conditions. The DFT calculations showed that at near physiological pH the complex formed by CaM(WT) with the neptunium ion is more stable than the one formed with uranyl.