Protein Structure from Scientific Research

Snapshot from MD simulations (Supplementary Video 4) of the apo D1 nucleotide binding pocket. Two Pi ions mimic the ADP·Pi state (transparent) and occupy the same positions as the β-P of ADP and the leaving Pi, bridged by a K+ or Na+ ion from the solvent. No Mg2+ ion is necessary to stabilize this arrangement in simulation or experiment.

DOI