Is it obligatory to withdraw the deposit from the bank because it is usurious, or can it be left there as long as there is no harm in it?

If the bank is usurious (Riba-based), it is not permissible to make a deposit with it, because this is Riba (usury), whether you take the interest or leave it for the bank in exchange for fees. Dealing with a usurious bank is not permissible except out of necessity, such as receiving one's salary and being content with a current account.