Figure 2.

Stereo diagram showing the structure of the RNase H primer grip. The RNA template strand is shown in turquoise, the DNA primer strand, in purple. The scissile phosphate is designated with a red arrow pointing to the phosphate. The RNase H domain is shown in orange; the connection subdomain is in yellow. Amino acids contacting the nucleic acid are labeled. Amino acids that were not mutated are labeled in black. Amino acids that had minimal (<2-fold) effects on titer when converted to alanine are labeled in green. Amino acids where alanine substitutions had a moderate (>5-fold) or strong effect on titer are labeled in blue. Contacts between individual amino acids and the RNA template are shown in black, contacts with the DNA primer are shown in red. Most of the contacts are shown as dotted lines; contacts with Q475 (which contacts both strands) are shown as solid lines. The nucleic acid strands are numbered relative to the site of cleavage on the RNA strand.