The large cleft in the middle is filled with DNA in the mouse DNMT1:
The catalytic core contains a mixed seven stranded beta-sheet that is flanked by three alpha helices on either side and at one end is joined by a two stranded anti parallel beta sheet from the BAH1 domain.
The TRD is also stabilized after folding by a Cys(3)His coordination of a Zn(2+) ion: