The zinc finger is a ~26 amino acid residue peptide that forms a structure which binds to specific sequences in DNA. We will use this structure to explore protein and DNA structure.

  Restrict the view to the entire domain of zinc finger 1. Using the dispaly function of the chime menu observe the domain in several different modes, including ball & stick, backbone, and cartoon. This domein is comprised of a hairpin made of two beta strands and an alpha helix. A zinc ion chelates the turn of hairpin and the alpha helix. Is the zinc ion at the C- or N-terminus of the alpha helix?


  Based on their structure, identify the amino acids that comprise the turn of the beta hairpin. (Remember hydrogens often are not depicted.)

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  Typically three or more zinc fingers are combined in one polypeptide to make a protein that recognizes a specific sequence of DNA bases. The structure we are exploring has 85 amino acid residues, which make three zinc fingers. The protein is bound to a short segment of DNA containing 11 base pairs.


What is the role of zinc in this protein? answer

Which secondary structure makes direct contact with what part of the DNA? answer

Which end of this structure contacts the DNA? answer

What sequence in which DNA chain is contacted by zinc finger 3? answer

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