2I13: Aart, A Six Finger Zinc Finger Designed To Recognize Ann Triplets

Cys2-His2 zinc fingers are one of the most common types of DNA-binding domains. Modifications to zinc-finger binding specificity have recently enabled custom DNA-binding proteins to be designed to a wide array of target sequences. We present here a 1.96 A structure of Aart, a designed six-zinc finger protein, bound to a consensus DNA target site. This is the first structure of a designed protein with six fingers, and was intended to provide insights into the unusual affinity and specificity characteristics of this protein. Most protein-DNA contacts were found to be consistent with expectations, while others were unanticipated or insufficient to explain specificity. Several were unexpectedly mediated by glycerol, water molecules or amino acid-base stacking interactions. These results challenge some conventional concepts of recognition, particularly the finding that triplets containing 5'A, C, or T are typically not specified by direct interaction with the amino acid in position 6 of the recognition helix.
PDB ID: 2I13Download
MMDB ID: 107427
PDB Deposition Date: 2006/8/12
Updated in MMDB: 2013/02
Experimental Method:
x-ray diffraction
Resolution: 1.96  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2I13: trimeric; determined by author
Molecular Components in 2I13
Label Count Molecule
Protein (1 molecule)
Aart(Gene symbol: Zscan2)
Molecule annotation
Nucleotides(2 molecules)
5'-d(*cp*ap*gp*ap*tp*gp*tp*ap*gp*gp*gp*ap*ap*ap*ap*gp*cp*cp *cp*gp*gp*g)-3'
Molecule annotation
5'-d(*gp*cp*cp*cp*gp*gp*gp*cp*tp*tp*tp*tp*cp*cp*cp*tp*ap*cp *ap*tp*cp*t)-3'
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB