Looks like the e46 one is e46 only, also there are a number of different types depending on whether the car is manual or automatic, if it has air con or not:
http://bmwfans.info/parts-catalog/E4.../cooling_unit/
OP, you'll have to be more specific than 01-03 e39, need to know engine, manual or auto, air con or not. Otherwise you could be buying the wrong part....