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Reuters journalists saw several men with shotgun wounds.
The army, which had pledged to protect demonstrators and keep rival factions apart, had troops in the area but violence only ended after some three hours when half a dozen armoured personnel carriers arrived and took up position on the bridge.
Islamists also took to the streets in cities across the country, including Assiut, Damanhour, Ismailia, and in the Nile Delta towns of Gharbeya and Beheira.
In the Sinai peninsula bordering Israel, where Egypt has struggled to control security since Mubarak was toppled, five police officers were gunned down in separate attacks in the town of El Arish, medical sources said.
Hardline Islamist groups have exploited a collapse in state authority after the uprising to launch attacks into Israel and on Egyptian targets.
The violence will ring alarm bells in the United States. Washington has so far avoided referring to the army’s removal of Mursi as a “coup”, a word that under U.S. law would require a halt to its $1.5 billion in annual aid.
Mursi’s opponents also say it was not a coup but an intervention to impose the “people’s will”.
The Brotherhood’s key political strategist, Khairat El-Shater, became the latest senior figure to be arrested since Mursi’s removal.
A legal technicality forced Shater’s withdrawal from the presidential campaign last year, promoting Mursi into being the movement’s candidate.
Brotherhood spokesman Gehad El-Haddad said the movement was faced with a crackdown from a state establishment unreformed from the days of Mubarak: “It’s the old police state of Mubarak with every ingredient and nightmare that it had before the Jan. 25 revolution. It’s as if we hit the reset button.”
But many Egyptians saw the military as a guarantor of stability at a dangerous time for the largest Arab nation of 84 million people.
“Maybe they will need to issue a curfew. Maybe the trouble will last a few days,” said Said Asr, 41, sitting with friends outside a Cairo cafe smoking a cigarette. “But the army is everything in this country. And they are taking control.”