Fig. 3 | Nature Communications

Fig. 3

From: RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution

Fig. 3

Examples of Arg76 conformations observed in MD simulations. The structure before (a) and after (b) the catalytic-like geometry is established. The base pairs on both sides of the scissile phosphate and Arg76 side-chain are shown as sticks, and the nearby backbone of helices B and preceding loops is shown as a wire representation. Arrows show 5′ to 3′ polarity of DNA strands. c Stacking between Arg76 and adenine base. Black arrows show 5′ to 3′ polarity of DNA strands. d Disruption of the base pair. e Flipping out of the adenine base. f Interactions that form with the scissile thymine. The blue arrows indicate the sequence of events. The dashed purple lines indicate H-bonds

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