McKinnon took part in his first day of team drills since injuring his right calf Aug. 9 before going down with a much more significant injury.
''He made a cut on air, no one was around him,'' coach Kyle Shanahan said before the MRI determined the severity of the injury. ''He went down. It looked awkward.''
The 49ers were counting heavily on McKinnon this season after signing him to a four-year, $30 million contract in free agency. The 49ers now have three healthy running backs on the roster in Matt Breida, Alfred Morris and Raheem Mostert.
McKinnon spent four years mostly as a backup in Minnesota. He has rushed for 1,918 yards with an average of 4.0 yards per carry, has 142 catches for 984 yards, and has scored 12 touchdowns.
The injury came hours before the 49ers had to reduce their roster to 53 players. The most notable cuts were defensive end Jeremiah Attaochu, who was signed as a free agent this offseason expected to boost the pass rush; Jonathan Cooper, who was expected to challenge for the starting right guard spot; and 2016 sixth-round pick Pita Taumoepenu.
The moves to cut Attaochu and Taumoepenu come as the Niners are still searching for consistent pass rushers on the outside. San Francisco kept 10 defensive linemen, with seven capable of playing outside, but none is a proven pass rusher.
Attaochu was slowed by injuries in training camp and wasn't able to show he could solidify that spot despite getting $2.5 million in guaranteed money when he signed his one-year deal this offseason.
''We just didn't get that many opportunities to correctly evaluate him,'' general manager John Lynch said. ''As you go into the regular season, dependability in terms of knowing when a guy will be out there is important. We made a tough decision but one we felt like we had to.''
The other players released Saturday were receiver Steven Dunbar Jr.; tight ends Ross Dwelley and Cole Hikutini; defensive backs Antone Exum Jr., Dexter McCoil, Tarvarus McFadden, Emmanuel Moseley and Tyvis Powell; running backs Malcolm Johnson, Jeremy McNichols and Jeff Wilson Jr.; offensive linemen Andrew Lauderdale, Coleman Shelton and Najee Toran; quarterback Nick Mullens; defensive lineman Niles Scott; and linebacker Korey Toomer.
The team also placed defensive lineman Kentavius Street on injured reserve and linebacker Reuben Foster and Victor Bolden Jr. on the suspended list. Foster will miss the first two games and Bolden is out for four games.
The Niners also could still place safety Marcell Harris and offensive lineman Erik Magnuson on injured reserve with the option to bring them back later in the season if they need another roster spot.
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