Fig. 2 | Nature Communications

Fig. 2

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

Fig. 2

Structural changes in MD simulations of the RuvC–DNA complex associated with the formation of catalytic-like geometry. a Close-up view of the active site of RuvC. Active-site residues and bases on both sides of the scissile phosphate are shown as blue and gray sticks for the MD simulations model and X-ray structure, respectively. Magnesium ions are shown as pink spheres. The black arrow indicates the motion direction of the scissile phosphate. b A new H-bond interaction between the protein backbone and scissile thymine formed in the simulations of the RuvC–DNA complex (purple). Helices B and preceding loops are shown in wire representation. Arrows show 5′ to 3′ polarity of DNA strands. c, d Pairing of the scissile T–A base pair. Arrows show 5′ to 3′ polarity of DNA strands. c A stable base pair in the crystal structure. d The broken base pair in MD simulations

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