Structures of phages homing nucleases in complex with Zn and dsDNA

Structures were predicted by AlphaFold3 on google servers at https://golgi.sandbox.google.com by introducing the sequence of the HNH protein, a Zn++ ion and a dsDNA of length between 26-32 base-pairs.

The predicted models report interactions between two residues of HNHs and the catalytic Zn++ ion as well as with the dsDNA. The HNHs N-terminal domain fits in a large dsDNA groove, bringing the Zn++ ion in the vicinity of the dsDNA backbone upper lip of the small groove. Except for HNH3, HNH4, HNH9 and HNH10, the C-terminal domain fits in the following large groove. The HNH3 and 4 C-terminal domain fits on the other side of the dsDNA. HNH9 and 10 do not possess a globular C-terminal domain. Between the two globular domains, a linker helix fits into the small groove between the two large grooves. To note, this linker helix harbours at its N-terminus one of the Zn++ ion binding residue.