DNA-binding proteins
Zinc fingers (PDB code 1ZAA, structure generated with PyMOL) are a common motif found in DNA recognition:
A zinc ion is coordinated between two histidine residues and two cysteines:
The other face of the alpha helix contains polar amino acids that hydrogen bond with the bases in the major groove of the DNA molecule.
Another means to interact with DNA is the leucine zipper (PDB code 1YSA):
Two alpha helices with leucines on the common face interdigitate, holding them together:
This allows the helices to clamp down like chopsticks on the DNA.
Catabolite activator protein (PDB code 1CGP), a dimer, in action binding to DNA:
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