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. Author manuscript; available in PMC: 2009 Nov 20.
Published in final edited form as: J Mol Graph Model. 2008 Nov 8;27(7):759–769. doi: 10.1016/j.jmgm.2008.11.003

Fig. 2.

Fig. 2

DNAP IV model showing the “chimney” and “roof” regions. Panel A: View from the minor groove side of DNAP IV (yellow), showing the “chimney” opening (cleft or hole), which is encircled by the upper lip (turquoise), left lip (blue) and lower lip (dark blue), along with +BP (red) emerging from the opening. The template (gray) and primer (brown) are also shown. The view in panel A is rotated approximately 180° to give panel B, which shows the chimney (white space) between the three chimney lips. Also shown are the roof-aa (S42, pink), which is a positionally conserved residue that lies above the nucleobase of the dNTP, the “roof-neighbor-aa” (S55, purple), which is next to the roof-aa and also contacts the dNTP nucleobase (dCTP, green), and the +BP (red), whose pyrene moiety must fit in the chimney in order for the dG moiety of +BP to pair with dCTP.