As soon as the villagers heard the gunshots, they came out pelting stones at the security personnel to breach the cordon.
The police said tear gas was used to disperse the protesters.
Doctors at the Shopian District Hospital where Magrey was taken said he had a bullet injury in the chest and had succumbed on the way to the hospital.
At least 10 other protesters were also injured in the clashes.
Authorities have shut down schools and colleges in Shopian on Wednesday to prevent violence by students.
Heavy deployment of police and paramilitary Central Reserve Police Force (CRPF) have been made in the city and other district headquarters to maintain law and order.
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