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Fig. 1 | Chemistry Central Journal

Fig. 1

From: Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand

Fig. 1

The proposed reaction mechanism for Tm1631–DNA complex. a Reaction area is encircled. The damaged nucleotide abasic dideoxyribose (3DR), which has no base (abasic site), is on position 7 of the 15 base pair long DNA chain. b Structure-based reaction mechanism of phosphodiester bond cleavage. The abasic site on the DNA is coordinated by the two Mg2+ ions, of which one also attacks the hydroxyl nucleophile (left panel). Pentacovalent transition state [2022] (middle panel) collapses, which leads to the cleavage of the scissile phosphodiester P-O3′ bond, with the transition state and the O3′ leaving group stabilized by the metal ion and inversion of the phosphate configuration (right panel)

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