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Figure 3
The kinked DNA structure. (a) DNA–box A contacts (NUCPLOT). Hydrogen bonds are shown as solid lines and nonbound contacts are shown as dashed lines. (b) Close-up views of the protein–DNA purine base interactions. Hydrogen bonds from residues Phe37 and Ser41 to base pairs A7 and G6 and a water-mediated hydrogen bond from Ser13 to A9 are shown in the upper and lower diagrams, respectively. (c) Comparison of DNA parameters for HMG-box intercalation sites. The roll and twist angles for box A in this structure were obtained with 3DNA, and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al., 1999BB38), 2gzk (box B; Stott et al., 2006BB51), 1qrv (HMGD; Murphy et al., 1999BB34), 1j5n (NHP6A; Masse et al., 2002BB70) and 3tmm (TFAM; Ngo et al., 2011BB36) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2). (d) Superimposition of box A kinked DNA (orange) with cisplatin-modified DNA (grey).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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