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A ring of threonines in the inner vestibule of the pore of CNGA1 channels constitutes a binding site for permeating ions

•  Cyclic nucleotide‐gated (CNG) channels are multi‐ion channels showing the anomalous mole fraction effect (AMFE) in the presence of Li+ and Cs+ mixtures. •  We show that Cs+ ions at the intracellular side of the membrane block the entry of Na+ ions in a voltage dependent way. •  The blockage is relieved when Thr359 and Thr360 at the intracellular entrance of the selectivity filter are replaced with an alanine. Moreover, the AMFE in the presence of intracellular mixtures of Li+ and Cs+ is abolished in T360A mutant channels. •  We have identified a second binding site – composed by the ring of Thr360 at the intracellular vestibule – in the selectivity filter of CNG channels controlling monovalent cations selectivity and permeation. •  These results help us understand fundamental similarities and differences between the pore of CNG channels and K+ channels.