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. Author manuscript; available in PMC: 2021 Feb 24.
Published in final edited form as: Methods Enzymol. 2018 Sep 27;615:285–332. doi: 10.1016/bs.mie.2018.08.017

Fig. 11.

Fig. 11

Dynamic transitions between the CIP and SIP states of the intermolecular ion pairs of Lys side-chain NH3+ and DNA phosphate groups observed in the 0.6-μs MD simulations for the Antp–DNA and Egr-1–DNA complexes. (A) The trajectories of the distances from the Lys Nζ atoms to the closest DNA phosphate oxygen atoms are shown for the intermolecular ion pairs for which the presence of CIP was experimentally confirmed. (B) Probability distribution of the CIP and SIP states as a function of the distance from the Lys Nζ atom to the closest DNA phosphate oxygen atom. (C) PMFs for the intermolecular ion pairs of the protein side-chain NH3+ and DNA phosphate groups in the Antp homeodomain–DNA complex and the Egr-1 zinc-finger–DNA complex.