The Key to the irons was a key that could lock and unlock the chains within the ships hold of the Flying Dutchman.
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When Carnby was captured by the pirates, they locked up both Grace and Carnby in the ships hold, and chained Carnby with the manacles. Grace was able to eventually find the key before becoming captured. Just before she was about to be chaiend up by one of the pirates, she threw the key over to Carnby who then freed himself and defeated pirate.
It was likely that when Elizabeth Jarret was incarcerated and locked in the hall, that she was chained up.