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. 2014 Feb 28;1(Pt 2):101–109. doi: 10.1107/S205225251400400X

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© Antonyuk et al. 2014

This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

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A simulated docking model of a short DNA fragment lying across the positively charged ‘groove’ on the surface of the PPD1 hexamer. The Fe–Mn site is located at the position of maximum positive (blue) charge density. The flexible N-terminal domain of the subunit of one trimer is poised above this site and the docked DNA strand sits adjacent to it. The surface-charge distribution is shown for pH 6 in units of kT/e⁻. Docking calculations were performed using the program Hex4.5 (Ritchie & Kemp, 1999 ▶). Surface electrostatic calculations were performed using the Adaptive Poisson–Boltzmann Solver (APBS; Baker et al., 2001 ▶) and were visualized using PyMOL. PDB2PQR (Dolinsky et al., 2004 ▶) was used to prepare the coordinates for input to APBS.