The scorpion toxin BeKm-1 is unique among a variety of known short scorpion toxins affecting potassium channels in its selective action on ether-a-go-go-related gene (ERG)-type channels. BeKm-1 shares the common molecular scaffold with other short scorpion toxins. The toxin spatial structure resolved by NMR consists of a short α-helix and a triple-stranded antiparallel β-sheet. By toxin mutagenesis study we identified the residues that are important for the binding of BeKm-1 to the human ERG K + (HERG) channel. The most critical residues (Tyr-11, Lys-18, Arg-20, Lys-23) are located in the α-helix and following loop whereas the “traditional” functional site of other short scorpion toxins is formed by residues from the β-sheet. Thus the unique location of the binding site of BeKm-1 provides its specificity toward the HERG channel.