Skip to main content
. 2006 Jan 3;4(1):e11. doi: 10.1371/journal.pbio.0040011

Figure 6. Details of Changes in Dpo4 Thumb Domain Contacts with Backbone Phosphates on the oxoG-Modified Template-Primer DNA Associated with the Nucleotide Binding and Incorporation Steps.

Figure 6

(A) Intermolecular contacts between the thumb domain (red) and the template strand (cyan) in the preinsertion binary complex. The phosphate groups interacting with Dpo4 amino acids are highlighted by shaded spheres. The phosphate group of T13 of the template strand is circled for reference.

(B) Intermolecular contacts between the thumb domain (red) and the primer strand (green) in the preinsertion binary complex. The phosphate groups interacting with Dpo4 amino acids are highlighted by shaded spheres. The phosphate group of A12 of the primer strand is circled for reference.

(C) Intermolecular contacts between the thumb domain (red) and the template strand (cyan) in the insertion ternary complex. The intermolecular contacts involving the thumb are retained on proceeding from the preinsertion binary complex (in A) to the insertion ternary complex (in C) on dCTP binding.

(D) Intermolecular contacts between the thumb domain (red) and the primer strand (green) in the insertion ternary complex. The intermolecular contacts involving the thumb are retained on proceeding from the preinsertion binary complex (in B) to the insertion ternary complex (in D) on dCTP binding.

(E) Intermolecular contacts between the thumb domain (red) and the template strand (cyan) in the postinsertion binary complex. The intermolecular contacts involving the thumb are translocated by one nucleotide step on proceeding from the insertion ternary complex (in C) to the postinsertion binary complex (in E) upon dCTP incorporation.

(F) Intermolecular contacts between the thumb domain (red) and the primer strand (green) in the postinsertion binary complex. The intermolecular contacts involving the thumb are translocated by one nucleotide step on proceeding from the insertion ternary complex (in D) to the postinsertion binary complex (in F) upon dCTP incorporation.