Supplementary Figure 2: Schematic diagram showing the interactions between Pol ɛ and the 11–16 primer template DNA.
From: Structural basis for processive DNA synthesis by yeast DNA polymerase ɛ
Residues interacting with DNA are color coded according to the domains they belong to (see Figure 1 for color coding). Residues in brackets indicate that these residues have side chains positioned in the vicinity of the DNA with the potential to form direct salt-bridges to the phosphodiester backbone. The first iodo-cytosine in the template DNA strand is not modeled in the structure and is shaded in white. Three base-specific contacts are indicated: the Nζ atom of K967 makes one base-specific hydrogen bond with the O2 atom of iodo-uracil 10, and the Nη1 and Nη2 atoms of R988 make base-specific hydrogen bonds to the N3 atom of guanine 8 and the O2 atom of iodo-uracil 7, respectively. The three nucleotides mentioned are all located in the primer strand. Water-mediated interactions between amino acids and the template bases are indicated with a red line and shown in Figure 5. The main-chain amino group of Y645 forms a hydrogen bond to the 3'-hydroxyl group on the deoxyribose moiety of the dATP
