This probably is a difficult topic and hard to establish with current knowledge, but maybe someone in the future will have more proof about Magdalene's ancestry.
According to some MyHeritage trees she was a daughter of Henning von Putbus, III and Kirsten Timmesdatter Krummedige but it's not been confirmed anywhere else.
At other internet trees, her parents remain unknown, but here maiden name is (von) Putbus as well. This leads to the conclusion, that most likely she was a descendant of the noble von Putbus/Podebusk family, so she might as well been in fact a daughter of previously mentioned Henning and Kirsten.
If anyone found something essential about Magdalene and her branch of Putbus family, please let me know.