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(covers information from several alternate timelines)
Alcatraz was an island in the San Francisco Metropolitan Area, California. This island was north of San Francisco's Fisherman's Wharf. One of the many notable structures on this island was a lighthouse.
In February 2259 of the alternate reality, this island, again unlabeled, was visible on a map of the bay. This map was part of a collection of graphics and video media that were seen on a powerwall in Admiral Christopher Pike's office at Starfleet Headquarters. Within days, the damaged USS Vengeance, on a course for Starfleet Headquarters, collided with the island, resulting in the destruction of the visitors center on the island. Seconds after this collision, the mortally wounded starship plowed into the bay, then regained altitude briefly before plowing into the city's waterfront. (Star Trek Into Darkness)
A version of Kathryn Janeway from the year 2404 told her past self in 2378 that one could see Alcatraz from USS Voyager's ready room on a clear day, because Voyager was a museum located on the Presidio in that timeline. (VOY: "Endgame")
Director J.J. Abrams described the destruction of Alcatraz as a reference to the cancellation of the TV series Alcatraz, which he served on as executive producer. (Star Trek Into Darkness iTunes enhanced commentary)
In the novelization of Star Trek Into Darkness, the impact with Alcatraz was what arrested the Vengeance's momentum enough to prevent the ship's hull from destroying Starfleet Headquarters, as Khan intended, though not enough to prevent the ship from crashing into the San Francisco waterfront.