Fig. 3

The modeling of the C-terminal domain (CTD) of DP2. a Top view of the PolD-PCNA-DNA complex. The crystal structure of DP1 and individual domains of DP2 were fitted as rigid body into the Form A map. The C-terminus of the CTD of DP2 crystal structure is indicated by the red arrow. The orange arrow indicates surplus region where elements corresponding to the crystal structure are not found. b Top view of PolD-PCNA-DNA (Form A). The CTD of DP2 was obtained by homology modeling (orange ribbon) and docked into the surplus region. c Bottom view (PCNA side) of the PolD-PCNA-DNA. The orange arrow indicates surplus region. d Bottom view (PCNA side) of the PolD-PCNA-DNA. The CTD and the Zn finger constructed and fitted by modeling are shown with an orange ribbon and red sphere atomic model, respectively. Slabs in the PCNA region are omitted for clarity for a to d. e Amino acid sequence of DP2 CTD and the predicted secondary structure (magenta: alpha helices, blue: beta sheet). The Zn-binding motif and the four zinc-coordinating cysteines are indicated by underline and asterisks, respectively