Identification of the DNA-Binding Domains of Human Replication Protein A That Recognize G-Quadruplex DNA
Figure 7
Comparison and prediction of ssDNA-binding sites. (a) Superposition of RPA-D (cyan) of with Pot1 (magenta). Alpha carbons from residue ranges of RPA2 residues, 130–142, 74–83, and 101–107 were superimposed with Pot1 (OB-1), 84–96, 23–32, and 56–62, respectively, with an RMSD of 0.8 Å. Pot1 residues 6–145 and RPA residues 43–171 are indicated as ribbons. DNA bases 1-6 (5′-TTAGGG-3′) from the Pot1 crystal structure are shown in green. (b) Superposition of Stn1 (yellow) with Pot1 (magenta). Alpha carbons from residue ranges 152–155, 122–127, 110–115, and 87–94 of Stn1 were aligned with residues 84–89, 56–61, 45–50, and 25–32 of Pot1, respectively, with an RMSD of 1.9 Å. Aromatic residues involved in stacking interactions from all proteins are shown as sticks. The superpositions of PDB entries 1XJV, 1QUQ, and 3KF8 were performed using ccp4i (LSQMK) [11] and displayed with Pymol (http://pymol.sourceforge.net/).
