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supplied The problem of acquiring a starting off docked structure equivalent to the experimental observations, we tried to manually strategy the Zn1-Zn2 fragment towards the DNA hairpin, by using CHIMERA manipulation tools.
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for this reason, we chosen the ideal docking configuration obtaining the correct orientation of Zn1-Zn2 with regard to your SSB ends, although this isn't the just one offering the ideal HADDOCK score and RMSD benefit. This configuration was then made use of because the setting up enter structure for an extended MD simulation of 0.six μs at T = 310 K. This starting up configuration has Zn2 interacting with nucleotides G1 (the \(five^ \key \)) and T23, the isolated nucleotide experiencing the SSB.
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