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. 2007 Jun 18;35(13):4275–4288. doi: 10.1093/nar/gkm416

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© 2007 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — (a,b) Definition of active site pocket geometry in closed ternary complexes: (a) minor groove side wall (defined by Ile-657, Glu-658, Tyr-714 and Gly-715) and width of pocket (measured by distance between C1′ of templating base and C1′ of incoming dNTP at insertion site); (b) floor (defined by flat face of base pair at post-insertion site) and ceiling (defined by Lys-706 and Phe-710) of pocket, and height of pocket on primer and template sides (measured by distance between Lys-706 Cα and carbon 6 of primer base at post-insertion site, and distance between Phe-710 Cα and carbon 6 of templating base at post-insertion site). (c) pocket wall in anti-[BP]G*:dCTP system at Step 2, deformed by BP (colored in red) on minor groove side. (d) Increase in pocket height on template side due to tilted plane of modified guanine in syn-[BP]G*:dC system at Step 4; syn-[BP]G*:dA and syn-[BP]G*:dT systems are similar. Also shown is an increase in pocket height on primer side in syn-[BP]G*:dC system. The single-head arrow indicates rolling motion in major groove edge of C. The BP moiety is again shown in red.