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4. Resistance to significant bending is outwardly because of the added contacts that both of those Zn fingers build, by pushing their facet loops (the a.a. seventeen–19 for Zn1, as well as the a.a 120–122 for Zn2) deep within the DNA grooves flanking the SSB hole, which forbid further more bending with the hairpin. It may anyway be speculated that, about a much longer time scale than the μs accessible to MD simulations, these ’side contacts’ could eventually bring about a forced bending. General, we noticed a very good correlation from the SSB hole opening With all the DNA bending angle, and also Together with the degree of regional undertwisting from the double helix.
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the typical framework obtained as the most beneficial cluster with the MD simulations was then made use of given that the setting up Zn2-DNA complicated, to further more dock the Zn1 monomer. An First configuration with Zn1 docked into the SSB hole is obtained from HADDOCK.