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. 2011 Sep 21;40(2):914–927. doi: 10.1093/nar/gkr749

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 6. — Surface analysis of TmMR^{NBD (S-S)}. (A) Superposition of the molecular surface of TmMR^{NBD (S-S)} and the PfMre11 bound branched DNA (PDB entry: 3DSD) (DNA colored in red; Mre11 and Rad50 are colored in blue and orange respectively; PfMre11 is not shown for clarity). While Rad50 blocks the Mre11 dsDNA-binding site in the ATP-bound state (left hand view), the surface shows holes between Rad50 and Mre11 that are in principle large enough to harbor ssDNA (right hand view). (B) Electrostatic surface potential of TmMR^{NBD (S-S)} in front and bottom view was calculated using APBS tools (55) and indicates positively (blue) charged patches located on the lateral side of Rad50 and along the Rad50 groove. The latter is suitable in size and charge complementary to dsDNA backbones.