Zinc Fingers

Exploring the Structure

When you go to the PDB to explore zinc fingers, try not to be overwhelmed: there are currently over a thousand structures containing all sorts of zinc fingers, knuckles, treble clefs, ribbons, and other fanciful folds. The structure shown here on the left, from PDB entry 1znf, shows a classic zinc finger. Since it's such a small structure, with only 25 amino acids, it's worth taking a closer look at what each part is doing. The two cysteines and two histidines are shown at the bottom, arranged in a tetrahedron around the zinc. Just above them, a phenylalanine and a leucine form a tiny hydrophobic core inside the small folded chain. The rest of the amino acids all face more-or-less outwards, and can be used for various functional tasks. For DNA binding proteins, the amino acids at the top of the alpha helix are typically used for recognition. This is shown on the structure at right, from PDB entry 1zaa. It contains three linked zinc fingers bound to DNA. The amino acids shown in red extend towards the DNA and read the base sequence, as shown in the lower figure where the DNA is removed.

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To see the publications that I used while writing this Molecule of the Month, click here. A list of 'Zinc Fingers' related entries in the PDB as determined by a keyword search on March 02, 2007 is also available.