Final answer:
The protein that binds cut DNA and retains it in a protein-DNA complex is XRCC4 with DNA ligase IV, part of the NHEJ pathway for repairing double-strand breaks in DNA.
Step-by-step explanation:
The protein that binds cut DNA and retains it in a protein-DNA complex is XRCC4 with DNA ligase IV. This is part of the non-homologous end joining (NHEJ) pathway which is a critical mechanism for repairing double-strand breaks in DNA. XRCC4 is a protein that facilitates the repair by bringing together broken DNA ends, stabilizing DNA ligase IV, and promoting the ligation of DNA ends. Additionally, the Ku70/Ku80 complex is involved in binding to the DNA ends and attracting other NHEJ machinery, the specific task of ligating the DNA is carried out by DNA ligase IV in complex with XRCC4.