DNA Polymerase: Structural Homology, Conformational Dynamics, and the Effects of Carcinogenic DNA Adducts
Figure 2
Stereoview (cross-eyed viewing) of Klentaq1 active site in the open binary (a) (PDB #4KTQ) and closed ternary (b) (PDB #3KTQ) conformations from the same view point [8]. (a) Open conformation: The O (yellow) an N (green) helices are in an open conformation allowing incoming dNTPs to reach the active site. The templating base (colored by element) is flipped out and Y671 (pink) occupies a stacked arrangement with the template (dark blue). (b) Closed conformation: The O and N helices have undergone a large conformational change and closed off the nucleotide binding pocket, which a ddCTP (colored by element with blue space filling) now occupies. The Y671 residue has flipped away from the template allowing the templating base to form a Watson-Crick base-pair with the ddCTP. The position of E615 allows screening of rNTPs via a steric clash with what would be a OH of an incoming rNTP. The metal ions A and B (green spheres) form interactions with the phosphates of the ddCTP, and Klentaq residues D610, 611 O, D785, and 2 waters (grey spheres). The missing binding partner of metal A is hypothesised to be the missing OH of the dideoxy-terminated primer terminus.
