Fig. 2

Structure of D4:DNA complex. a. Schematic diagram of the D4-DNA interactions. Bases are represented by one-letter codes (colored: A red, T blue, G green, C brown) and base pairs are connected by a solid black line (note that DA4 and DT29 form a non-WC base pair). The DNA backbone is drawn next to the bases (sugars as brown pentagons; phosphates as purple circles). DNA strand 1 (chain C) runs from top (5’) to bottom while the complementary strand 2 (chain D) runs in the opposite direction. Base numbers as in the PDB coordinate file are written inside the sugars. Interactions are plotted on either side of the strands; interacting protein residues are represented by their atom name (O in red, N in blue), residue name and number (chain identifier in parenthesis). Blue (dotted) lines represent hydrogen-bonded contacts (3.9 Å cut-off between ‘heavy’ atoms as defined in PDBePISA). Circles (in cyan) labeled ‘W’ indicate water-mediated interactions with DNA. Water molecules are labeled by their PDB number. Protein interactions of subunits A and B with DNA strands C and D are highlighted as boxes and labeled. NUCPLOT (http://www.ebi.ac.uk/thornton-srv/software/NUCPLOT/) [49] was used to generate the figure. b. DNA binding site in D4:DNA complex. Cartoon diagram illustrating the D4 chains A and B in light pink and light cyan and the corresponding DNA chains in pink (D) and bluish green (C) respectively. Location of the partially disordered ‘Leu-intercalation loop’ is labeled as Leu-loop and indicated with dotted lines. c. Molecular surface for D4:DNA complex. Molecular surface of the two D4 subunits is shown with the overlaid electrostatic potential contoured from negative (red) to positive (blue) [−10 kBT/e to +10 kBT/e]. The DNA helix is displayed as cartoon drawing (color: P yellow, O red, N blue, C grey). This figure was generated using UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) [50]