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Snapshot of the KSI active site for the Intermediate state shown in Figure 1. The snapshot was obtained from the MD simulation of the first proton transfer step with the mapping potential corresponding to λ = 0.95. The proton has transferred from the substrate to Asp38, and residues Tyr14 and Asp99 are hydrogen bonded to the substrate, which is in the dienolate form. The transferring hydrogen is identified with an asterisk.
