Fig. 6: Conformational switching of XPD’s domains during the ATPase cycle causes dramatic changes in the ssDNA binding interactions. | Nature Communications

Fig. 6: Conformational switching of XPD’s domains during the ATPase cycle causes dramatic changes in the ssDNA binding interactions.

From: Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology

Fig. 6

Zoomed-in views of the DNA-binding groove of XPD show the evolving contacts between XPD and ssDNA across four functional states: (a) S1, (b) S4, (c) S5, and (d) S7. Panels on the left show the DNA binding cleft with bound ssDNA (cyan) and XPD domains colored as follows: RecA1 (gold), RecA2 (blue), Arch (magenta), and Fe–S (green). Key residue contacts to ssDNA are shown explicitly in atomic (ball-and-stick) representation. Side chains of interacting residues are colored by domain. Constriction 1, Constriction 2, and their engagement to ssDNA are shown schematically on the right-side panels, which also depict ssDNA interactions identified by persistent contact analysis of the four macrostates. The reorientation of the Arch domain in the ATP-bound state is shown in panel (b).

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