JERUSALEM—Tensions were running high at a disputed Jerusalem holy place on Friday as Palestinians gathered for Muslim prayers under tight Israeli security.

Nearly 3,000 Israeli police and soldiers deployed in and around Jerusalem’s Old City as Israel reopened the Mosque of Al-Aqsa, the site Jews call the Temple Mount.

The ancient compound marks the holiest place in Judaism and third holiest in Islam, and it is a flashpoint of the Israeli-Palestinian conflict.

Israel closed the mosque Thursday amid growing unrest after police killed a suspected Palestinian gunman in a nearby Arab neighborhood.

The suspect had allegedly shot and critically wounded right-wing Israeli rabbi Yehuda Glick, who advocates Jewish prayers at the disputed holy place and even the rebuilding of the biblical Temple there.

Palestinians called for a “day of rage” on Friday, so in a bid to prevent further riots, Israel barred Palestinian men under the age of 50 from entering the Al-Aqsa compound.

Israeli Prime Minister Benjamin Netanyahu defended the crackdown, saying riots in Jerusalem will not be tolerated.

Netanyahu blamed radical Islamic elements and Palestinian President Mahmoud Abbas for what he described as a “wave of incitement” to violence. He said Israel will do whatever is necessary to restore calm.

U.S. Secretary of State John Kerry urged both sides to “exercise restraint…and preserve the historic status quo” at the Mosque of al-Aqsa and Temple Mount.

Even with the heavy security presence and a steady rain, Palestinians and Israeli security forces clashed in the West Bank late Friday.

Palestinians protested near Hebron and the Qalandiya checkpoint after Friday prayers, calling for a “day of rage,” and Israeli troops responded with tear gas and stun guns.

There were no immediate reports of casualties.

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