SANTA CLARA – Running back Jerick McKinnon went down with a knee injury on Saturday that has the 49ers concerned he could have sustained a season-ending ACL injury.

“We hope that we’re wrong,” 49ers coach Kyle Shanahan said Saturday afternoon on a conference call with Bay Area reporters.

McKinnon returned to 11-on-11 drills Saturday for the first time since sustaining a calf injury three weeks ago. On the final play of practice, he went down with what appeared to be a serious knee injury.

“He just made a cut on air and no one was around him and just went down,” Shanahan said. “It looked awkward. We’re concerned about it, but we don’t have an MRI done, so we don’t know for sure.”

McKinnon was scheduled for an MRI on Saturday afternoon. The injury occurred before the 1 p.m. deadline to submit cuts for the 53-man roster. The 49ers kept McKinnon on their initial 53-man roster.

“We’re concerned, but we’re also confident,” 49ers general manager John Lynch said. “We have a lot of good football players here. We’re proud of our 53-man roster. Next week we’re going to be really excited, looking to take on the Vikings.”

The 49ers open the regular season on Sunday, Sept. 9, against the Minnesota Vikings, McKinnon’s former team. The 49ers signed McKinnon to a four-year, $30 million contract on the first day of free agency. He was expected to be one of the central figures of the team’s offense, as a runner and receiver.

The 49ers kept three other running backs, along with fullback Kyle Juszczyk on their roster. Veteran Alfred Morris, who was signed two weeks ago, could be the starter when the 49ers open the season. Matt Breida is likely to be the backup, with special-teams ace Raheem Mostert available in emergency situations.