Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2007 Jul 25;35(15):5096–5107. doi: 10.1093/nar/gkm545

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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.

PMC Copyright notice

Figure 4. — Modelling of nascent 8oxodG(anti):dC and 8oxodG(syn):dA base pairs in the polymerase active site. Modelling an 8oxodG(syn):dA base pair shows the steric hindrance between the O⁸ atom and the surface formed by ϕ29 DNA polymerase residues Tyr390 and Gly391, according to (20). van der Waals surfaces are shown for base pairs (light brown) and for protein side chains (coloured according to their electrostaticity). 8oxodG(anti):dC [coordinates obtained from PDB1 Q9Y (20)], and 8oxodG(syn):dA [PDB1 TK8 (19)] base pairs were first modelled into RB69 DNA polymerase active site (PDB1 IG9). Superposition of RB69 and ϕ29 (PDB1 XHX) DNA polymerase active sites allowed us to model both base pairs at the active site of the latter. Green dotted lines represent the potential hydrogen bonds formed between the nucleotides.