1. Slide 1 Powerpoint Assignment for Micbio 565 Eric Martz Yeast Gal4 transcriptional regulator, 1d66. X-ray crystallography, resolution 2.7 Angstroms. 2 protein chains + 2 DNA chains (total 4)

2. Slide 2: PQS The published PDB file has 4 chains. PQS says “dimeric complex”, meaning a protein dimer complexed to DNA (still 4 chains). Published PQS

3. Slide 3: Ligands AbbreviationFull Name CDCadmium ion

4. Slide 4: Hydrophobic/Polar This protein has a mostly polar surface, consistent with it being water soluble. There are no large hydrophobic patches on its surface.

5. Slide 5: Charge The DNA-binding notch in the protein has only positive charge, consistent with the need to bind the negatively- charged phosphate backbone of the DNA.

6. Slide 6: Conservation (ConSurf) The amino acids that contact the major groove of the DNA are highly conserved. This is where Lysine 18 (highlighted) recognizes the specific DNA sequence CGG.

7. Slide 7: Animation from Polyview-3D Lysine 18 in Gal4 sits in the major groove of DNA, recognizing the DNA sequence CGG. This animation was kept small to minimize the load on the Polyview-3D server. It rocks through 90 degrees in 2 degree steps, with a 5/100 second delay.

8. Optional Slide 8: Noncovalent Bonds 6 cysteine sulfurs form a cage around the two cadmium metal ions.