Is it permissible to work for a company whose funds are held in a usurious bank, while avoiding usurious transactions, knowing that a portion of the company's capital comes from usurious surpluses?

If the worker's job is not related to usury or assisting in it, then there is no harm in it, even if the company deposits its money in an interest-based bank, or if the shop owner has taken an interest-based loan. This is because dealing with mixed wealth is permissible as long as the worker's job is far from usury and other forbidden matters.