Figure 2: R.PabI–DNA interaction.
From: A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi
(a) Stereo view of the unwound DNA. Guanine, thymine, adenine and cytosine bases of the R.PabI recognition sequence are shown using blue, pink, purple and green stick models, respectively. R.PabI residues of the β8–β9 loop are shown using a cyan stick model. Hydrogen bonds are indicated by blue dotted-lines. (b) Intermolecular hydrogen bonds between R.PabI and the DNA duplex. The hydrogen bonds are indicated with lines. Residues from R.PabI protomers A and B are indicated by orange and blue, respectively. (c) The composite omit map (2 σ) around the R.PabI recognition sequence is shown by blue mesh. The structure of the R.PabI–DNA complex is shown using a stick model.
