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Saudi officials said that the 47 executions were carried out at 12 sites after convictions for terror acts.
Some were convicted of plotting and carrying out attacks against civilians going back as far at an attack on the U.S. Consulate in Jeddah in 2004.
Nimr was arrested in 2012 following what Saudi authorities described as a car chase in which he rammed a vehicle used by security forces and resisted arrest.
His family and other critics have disputed the government's account.
Human rights advocates, including the United Nations Office of the High Commissioner for Human Rights, have called for his conviction to be overturned, as well.
His supporters say Ali al-Nimr was a juvenile when he was arrested and was tortured into confessing to crimes.