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Vaughn spent the 2015-16 season in the San Antonio Spurs’ front office as a pro personnel director.
Vaughn, 41, was fired as the Magic’s coach in February of 2015, with a 43-121 record in three-plus seasons. He had been an assistant coach with the Spurs prior to taking the Orlando head coaching job in 2012.
Atkinson, the top assistant with the Atlanta Hawks, will finish that franchise’s playoff run before starting his duties in Brooklyn.
Brooklyn general manager Sean Marks worked closely with Vaughn during their shared time together with the Spurs.