Fig. 3

Oxygen atoms of P71, D75 and D501 coordinate cations. a Total time that K⁺ and Na⁺ stay in the coordination site during each of the three simulations expressed in percentage. b Coordination of cations happens via the backbone oxygen atom of P71, one side chain oxygen atom of D75 and both side chain oxygen atoms of D501 (red spheres). Average ion-atom distances for sodium and potassium are indicated in the figure. Sodium: 1) 2.38 ± 0.14 Å, 2) 2.29 ± 0.09 Å, 3) 4.02 ± 0.21 Å, 4) 2.90 ± 0.65 Å, 5) 2.58 ± 0.31 Å and 6) 3.74 ± 0.25 Å. Potassium: 1) 2.74 ± 0.19 Å, 2) 2.63 ± 0.30 Å, 3) 4.15 ± 0.40 Å, 4) 2.92 ± 0.47 Å, 5) 2.90 ± 0.38 Å and 6) 3.96 ± 0.28 Å. c Exemplary plot of ion-atom distances for sodium. Distances of one sodium ion and all six charged atoms facing the potential coordination site are represented for 5 ns of MD system 1 while Na⁺ is inside the pocket. The close proximity (< 2.5 Å) of Na⁺ to the backbone oxygen of P71, one side chain oxygen of D75 and both side chain oxygen atoms of D501 is illustrated, indicating their ability to coordinate sodium