Figure 2.

PRDM9c ZF8–13 form base-specific interactions. A, schematic representation of ZF8–13 interactions with DNA. The top line indicates the 18-bp consensus sequence. The second line indicates the base pair positions (positions 0–19). The third and the fourth lines are the sequence of the double-stranded oligonucleotide used for crystallization, shown with the top strand matching the consensus sequence. Amino acids of each finger interact specifically with the DNA bases, as shown below. B, DNA base-specific interactions involve a particular residue of each ZF. Atoms are colored dark blue for nitrogen and red for oxygen, and carbon atoms are decorated with finger-specific colors according to Fig. 1F. The numbers indicate the interatomic distance in angstroms (between protein and DNA). For clarity, the H-bond distances for Watson–Crick base pairs are not shown. w, water molecules (small red spheres). C, His⁷³³ interaction with G2. D, Arg⁷³⁶ interaction with G3. E, Arg⁷⁵⁷ interaction with G4. F, His⁷⁶¹ interaction with G5. G, Ser⁷⁶⁴ is positioned too far away from T6. H, Asp⁷⁸⁶ interaction with C7. I, Asn⁷⁸⁹ interaction with A8. J, Ser⁷⁹² forms a weak H-bond with C9. K, Trp⁸¹⁴ forms a π–methyl interaction with the T10 methyl group. L, Val⁸¹⁷ forms a van der Waals contact with C11. M, Arg⁸²⁰ interaction with G12. N, Asp⁸⁴² and Ser⁸⁴⁴ interaction with the G13:C13 base pair. O, Asn⁸⁴⁵ interaction with A14. P, Ser⁸⁴⁸ is too far away from A15. Q, Asn⁸⁷⁰ and Ser⁸⁷² are positioned too far away from the G16:C16 base pair. R, His⁸⁷³ interaction with G17. S, Arg⁸⁷⁶ interaction with G18.