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Mr Mekki, 58, said he had tried to resign on 7 November but that circumstances had forced him to remain.
BBC: Egypt vice-president resigns on final day of referendum
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On Sunday, Mr Mursi also appointed Mahmoud Mekki as vice-president, a senior judge who fought for judicial independence under Hosni Mubarak.
BBC: Egypt President Mursi explains army chief replacement
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The Egyptian justice minister, Ahmad Mekki, has condemned the lynching and killing.
BBC: Egyptian villagers lynch two men
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"It is the state's responsibility to do justice and see that justice is done and provide security for its people, " Mr Mekki added.
BBC: Egyptian villagers lynch two men
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The BBC's Shaimaa Khalil in Cairo says Mr Mekki appeared to be giving the impression that he was unhappy with not being consulted on key decisions.
BBC: Egypt vice-president resigns on final day of referendum
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Morsy appointed Mekki to the post earlier this year.
CNN: Egypt's VP resigns amid vote over draft constitution
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Cairo, Egypt (CNN) -- Egyptian Vice President Mahmoud Mekki is stepping down from his post, state-run Nile TV announced Saturday, amid a second round of voting on the country's Islamist-backed draft constitution.
CNN: Egypt's VP resigns amid vote over draft constitution
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"I realized since taking the position that the nature of the political duties does not suit my professionalism as a judge, so I submitted my resignation on November 7, " Mekki said on his Facebook page.
CNN: Egypt's VP resigns amid vote over draft constitution
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Mekki said he resigned last month, but stayed on because he had to tend to a number of important issues, including the controversy over the new constitution, according to his resignation letter published by the state-run MENA news agency.
CNN: Egypt's VP resigns amid vote over draft constitution
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He also named Mahmoud Mekki as his vice president, and he reversed a June constitutional decree by the Supreme Council that claimed to retain legislative authority until a new parliament could be sworn in near the end of the year, Ali said.
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