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We performed a number of distinct HADDOCK docking experiments, where Zn1 was approached towards the \(five'\) close of the Zn2-DNA intricate at various time frames on the MD simulation. In the subsequent, we show two representative scenarios at times t = two ns (Fig.

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We produced two separate PDB buildings by isolating the protein as well as DNA hairpin from your RCSB PDB entry 2N8A, which were being then reassembled by docking with HADDOCK. The Lively residues to bootstrap the docking were being: the residues Phe-forty four and Leu-151 in the protein (belonging to Zn1 and Zn2 respectively), and the nucleotides G1 (\(five^ \key \) conclude of your hairpin), G45 (\(3^ \prime \) conclude), plus the T23 (unpaired base struggling with the SSB gap) on the DNA. This resulted in docked clusters obtaining a lot of the interactions that were presently proven in the experimental NMR construction. Then, we picked the most beneficial docking pose depending on the RMSD value as Original configuration, and carried out a 200-ns MD simulation at T = 310 K (Fig.

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regarding the t = four hundred ns docking, the initial arrangement of Zn1 and Zn2 appears to remain tiny altered for The entire 50 0ns MD; as a consequence of their mutual interaction, equally zinc fingers seem to have a decreased interaction With all the SSB gap. even so, a fascinating info attained through the plots of this simulation in Fig. 6c includes the DNA bending angle quickly evolving toward very smaller angles, about \(a hundred and twenty^ \circ \) in the second Section of the trajectory, when concurrently the SSB gap continues to be very closed at twelve-thirteen nm.

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