Dozens of Palestinians were wounded by tear gas and rubber bullets, medics said.
The resolution also called for an end to the demolition of Palestinian homes and EU-funded structures and projects, the forced displacement of Palestinian families and the confiscation of Palestinian property in the West Bank.
Hundreds of Palestinians had gathered at the Huwara checkpoint, south of Nablus and the site of repeated clashes between Israeli soldiers and Palestinian stone-throwers.
Following the shooting, the Israel Defense Forces broke up the mob using non-lethal riot-dispersal methods, according to reports.
Two Palestinian were seriously wounded by live fire near Khan Younis in the southern Gaza Strip, the Palestinian Health Ministry said.More news: Everything you need to know about the 'WannaCrypt' ransomware attack
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The so-called "Freedom and Dignity" strike, orchestrated by imprisoned Fatah member Marwan Barghouti, has sparked a number of demonstrations across the West Bank since it began on April 17.
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A second was shot by a settler on Thursday after his vehicle was pummeled by rocks and projectiles driving through a large demonstration near Harawa, claiming he was "about to be lynched" by the Palestinian protesters. "The prisoners are very determined and prefer to die in dignity rather than continue to be imprisoned in inhumane conditions", Shawan Jabarin, the director of the internationally-renowned Palestinian rights group Al Haq, based in Ramallah in the West Bank, told the African News Agency (ANA) during an interview earlier in the week.
He held Israel responsible of any consequences or harm that would occur to the prisoners and their life, adding that the Palestinian leadership "is holding high-level contacts to pressure on Israel to meet the prisoners' demands".
In December, the Israeli government lashed out over a UN Security Council resolution that condemned Israeli settlement building in the Palestinian Territories and called on Israel to stop immediately.