The zinc finger (DNA binding site) of transcription factor Zif268/DNA complex
Mus musculus (house mouse)
There are a few recurring motifs found in proteins that interact with DNA. The three most important ones are the helix-loop-helix, the leucine zipper and the zinc finger motif. Proteins that contain zinc finger domains are often involved in gene regulation and they were first discovered as part of a transcription factor protein. The typical structure of a zinc finger is a two-stranded anti-parallel beta sheet followed by a helix. The helix runs approximately parallel to the direction of the sheet. The top of the sheet, near the turn between the two strands, contains two cysteines and the end of the helix that comes close to this turn, contains two histidines. The two cysteines and the two histidines together coordinate one zinc ion, which lies sandwiched between the beta sheet and the helix. This is the standard arrangement of a zinc finger.
In the example here we see a small protein, with 87 residues, that is made from 3 consecutive zinc fingers which consist of the DNA binding site of the transcription protein Zif268. The 3 zinc fingers of the protein are arranged to form a roughly U-shaped cleft. Within this cleft, lies the DNA bound to the protein. When viewed from the side with the DNA axis pointing upward, one can see, that the helices of the three zinc fingers are deeply embedded into the major groove. The orientation of each zinc finger domain changes to follow the twist of the DNA helix as it winds forward, making it almost appear like a 3-stranded helix with two of the strands formed by DNA and the third strand by the protein.
Protein Data Bank (PDB)
author: Arno Paehler