The Mint deposits the newly minted coin(s) at the Federal Reserve, or alternatively, sells them directly to financial investors and the public, who can then deposit them at their own commercial banks, which in turn can deposit them at the Federal Reserve.
In both cases, the Mint is credited for the full nominal face value of the coins via its dedicated reserve account at the Fed, and the coins end up being held as assets on the Fed's balance sheet, along with the trillions of dollars of Treasury securities it already holds.
Source: Federal Reserve Bank of St. Louis