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Figure 7
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, 1999BB44). Surface electrostatic calculations were performed using the Adaptive Poisson–Boltzmann Solver (APBS; Baker et al., 2001BB2) and were visualized using PyMOL. PDB2PQR (Dolinsky et al., 2004BB11) was used to prepare the coordinates for input to APBS.

IUCrJ
Volume 1| Part 2| February 2014| Pages 101-109
ISSN: 2052-2525
doi:10.1107/S205225251400400X