The structure files linked to this page show the four major motifs found in DNA-binding proteins.
The first file shows the helix-turn-helix motif. It consists of two segments of alpha helix separated by a short irregular region, or "turn". The more C-terminal helix lies in the major groove of the DNA double helix. Contacts between the amino acid R-groups of this helix and the nucleotides of the groove determine the sequence specificity of the DNA binding.
The second file shows the helix-loop-helix motif. It consists of a short segment of alpha helix connected to a longer segment of alpha helix by an irregular region, or "loop". Part of the motif is a dimerization domain that interacts with other helix-loop-helix proteins to form of homo- or heterodimers. The partner used determines DNA binding affinity and specificity. Two sections of alpha helix, one from each monomer, bind to the major groove of the DNA double helix.
The third file shows the leucine zipper motif. Proteins of this type form homo- or heterodimers. Two alpha helices, one from each monomer, form a coiled-coil structure at one end due to interactions between leucines that extend from one side of each helix. Beyond the dimerization interface the alpha helices diverge, allowing them to fit into the major groove of the DNA double helix. The dimerization partner determines DNA binding affinity and specificity.
The fourth file shows the zinc finger motif. It consists of a segment of alpha helix bound to a loop by a zinc ion. The zinc ion is held in place by two cysteine and two histidine R groups. The alpha helix lies in the major groove of the DNA double helix. Zinc finger motifs are often repeated in clusters.