Introduction - This script shows how transcription factors interact with DNA. Scroll down until the text corresponding to the view is visible.
One common motif for a DNA-binding protein is the helix-turn-helix. The recognition helix (DNA-binding helix) is GREEN, the turn is BLUE and the other helix is REDORANGE. (Based on 1lcd.pdb, V.P.Chuprina et al., J. Mol. Biol. 234 446 (1993)).
This is a leucine zipper DNA-binding protein. Note how the two long alpha helices interact with the DNA. (Based on 1ysa.pdb, T.E.Ellenberger at al., Cell 71 1223 (1992)).
In a leucine zipper DNA-binding protein the two helices are held together by hydrophobic interactions between, mainly, leucine sidechains (BLUE).
This is a zinc-finger DNA-binding protein (GREEN). The zinc (MAGENTA) coordinates to the protein to create the DNA-binding helix (YELLOW). (based on 1glu.pdb, B.F. Luisi et al., Nature 352 497 (1991)).
This is a restriction enzyme, EcoRV (GREEN) bound to its target DNA. (Based on 4rve.pdb, F.K.Winkler et al., EMBO J. 12 1781 (1993)).
Note how binding of EcoRV bends the DNA toward the major groove.