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Bacteria use specialized proteins, like transcription factors, to rapidly control metal ion balance. CueR is a Gram‐negative bacterial copper regulator. The structure ofE. coliCueR complexed with Cu(I) and DNA was published, since then many studies have shed light on its function. However,P. aeruginosaCueR, which shows high sequence similarity toE. coliCueR, has been less studied. Here, we applied room‐temperature electron paramagnetic resonance (EPR) measurements to explore changes in dynamics ofP. aeruginosaCueR in dependency of copper concentrations and interaction with two different DNA promoter regions. We showed thatP. aeruginosaCueR is less dynamic than theE. coliCueR protein and exhibits much higher sensitivity to DNA binding as compared to itsE. coliCueR homolog. Moreover, a difference in dynamical behavior was observed whenP. aeruginosaCueR binds to thecopZ2DNA promoter sequence compared to themexPQ‐opmEpromoter sequence. Such dynamical differences may affect the expression levels of CopZ2 and MexPQ‐OpmE proteins inP. aeruginosa. Overall, such comparative measurements of protein‐DNA complexes derived from different bacterial systems reveal insights about how structural and dynamical differences between two highly homologous proteins lead to quite different DNA sequence‐recognition and mechanistic properties.