Above: Electron density map calculated using observed amplitudes and phases calculated from the protein coordinates alone and contoured at 1σ.The observed DNA substrate is depicted using a stick representation. Below: The primer and template strands are colored grey and wheat, respectively. The bases are represented as rounded rectangles with the phosphate backbone represented as yellow circles. The 3’ primer terminal ddC base is colored blue and the incoming nucleotide is colored red. The numbering used to identify specific bases is indicated in black above the template strand. The two bases of the substrate that are not observed in the crystal structure at the −20 and −21 positions are rendered transparent.

(A) Surface representation of interactions between the Thumb domain of PolIIIα with the DNA substrate in cartoon representation. Green surfaces indicate the Thumb domain with blue surfaces representing residues proposed to interact with the DNA substrate. Yellow surfaces represent the PHP Nuclease domain. The polymerase active site is seen at left as demarcated by the blue stick representation of the 3’ Primer Terminal Base (ddC) and the red stick representation of the incoming nucleotide (dATP).
(B) Surface representation of interactions between the β-binding domain of PolIIIα with the DNA substrate in cartoon representation. Orange surfaces indicate the β-binding domain with three key loops implicated in DNA binding colored as follows: Taq927 – Taq923 (blue), HhH motif Taq892 – 910 (cyan), and Taq846 – Taq852 (pruple). Positively-charged residues that are within proximity to interact with the sugar-phosphate backbone and labeled and their positions are indicated with white arrows. An additional arrow points to the location of the polymerase active site.
(C) The observed DNA substrate of PolIIIα is depicted using a cartoon representation with the primer strand colored white and the template strand colored wheat. Idealized B-form DNA aligned with the DNA substrate prior to bending is displayed in a surface representation. Black lines indicate the helical axes of the DNA substrate (outside of the active site) and the idealized B-form DNA. The 3’ primer terminal base is represented in blue sticks. The loops of the thumb domain (Taq492 – Taq499 and Taq569 – 575) that induce DNA bending are colored green and represented as a surface.

(A) The two sheets of the palm domain which contain the catalytic aspartate residues are depicted in a cartoon representation. The catalytic residues and sheets of the palm domains of Eco PolIIIα, Taq PolIIIα, and Polβ are colored grey, pink, and green, respectively. The catalytic aspartates are depicted as sticks and are labeled as follows: “1” represents Eco401,Taq463 and D190 of Polβ; “2” represents Eco403, Taq465 and D192 of Polβ; and “3” represents Eco555, Taq618 and D256 of Polβ.
(B) The palm domain of Eco PolIIIα in relation to the DNA substrate of Taq PolIIIα when including the third catalytic carboxylate as a reference for superposition of the palm domain of Eco PolIIIα onto that of Taq PolIIIα. The DNA substrate is depicted as in Figure 1. The Eco palm is colored gray. The active site helix is colored magenta. A mainchain clash between the active site helix of Eco PolIIIα and the DNA substrate of Taq PolIIIα is indicated by a white arrow. Sidechains closest to the DNA substrate are depicted as spheres.
(C) A superposition of the palm domains of Eco and Taq PolIIIα when the third catalytic carboxylate is omitted as a reference.

(A) A view of the crystal structure of the replicating complex of Taq PolIIIα. Domains are labeled as follows: PHP Nuclease (yellow), Palm (pink), Thumb (light green), Index Finger (light blue), Middle Finger (dark blue), β-binding (orange) and C-terminal (red). The template and primer strand are represented as spheres and colored wheat and white, respectively. The 3’ primer terminal base is depicted with blue spheres and the incoming nucleotide is depicted with red spheres. PolIIIα is depicted in a cartoon representation. The density for the downstream DNA template strand is represented in mesh.
(B): A close-up of the active site of PolIIIα. PolIIIα is depicted using a surface representation. The DNA substrate is depicted as sticks and colored as in the left panel. The incoming nucleotide and 3’ prime terminal base are colored red and blue, respectively. Key active site residues are colored as follows: D463, D465 and D618 are colored red, K616 is colored yellow, S426 is colored green, and R767 is colored blue. The Active Site Helix is colored magenta.

(A) Cartoon Depiction of domain changes in PolIIIα associated with binding of DNA substrate. Domains are colored as in figure 2. Colored arrows indicate the direction of domain movement. Domain positions from the unliganded PolIIIα structures are presented in a cartoon representation and colored grey.
(B) Changes in the position of the OB-fold associated with binding of DNA substrate. The positions of the OB-fold of PolIIIα in unliganded and ternary complex conformations are shown in a cartoon presentation and colored grey and red, respectively. Here, the very C-terminus of the C-terminal domain and the β-binding domain are omitted for clarity. The density for the downstream DNA template strand is represented in mesh.
(C) The polymerase active site in the structure of the ternary complex of PolIIIα. The DNA substrate, the 3’ primer terminal base, metals and the incoming nucleotide are colored as in Figure 2. The 3’ primer terminal base and incoming nucleotide are represented as sticks. The five β-sheets of the palm domain and the DNA substrates are displayed in a cartoon representation and colored pink and wheat (template) and white (primer), respectively.
(D) The polymerase active site in the structure of the ternary complex of Polβ.

(A) The polymerase and duplex DNA substrates are represented and colored as in Figure 1. The clamp is shown in a cartoon representation and colored purple. The polymerase binding sites on the clamp are colored cyan and depicted in a sphere representation.
(B) Here, the model of two polymerases simultaneously bound to the sliding clamp is depicted with PolIII and PolIV in surface representation and colored as in Figure 2 and green, respectively and rotated about the helical axis of the DNA into the page by about 60°. The clamp is depicted in a cartoon representation and colored purple. The position of PolIV was achieved using a model of the little finger domain of E. coli Pol IV bound to clamp (PDB ID: 1UNN) (Bunting et al., 2003) and the structure of the ternary complex of Pol IV (PDB ID: 1JXL).(Ling et al., 2001) and the same modeling procedure as in (Indiani et al., 2005).