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A tentative calm had settled on the Heliopolis streets surrounding the presidential palace by early Thursday after a night of rock throwing and fighting between the president's supporters and opponents.
At least five people have been confirmed dead, according to doctors and state news sources. State-run MENA news agency reported 446 injured.
Several armored personnel carriers and tanks were deployed in the area Thursday morning as about 2,000 Muslim Brotherhood members continued to chant pro-Mohamed Morsy slogans, eyewitnesses told Egypt Independent.
Members of the presidential guard could also be seen in the streets surrounding the palace.
Opposition protesters marched on the palace Tuesday to pressure Morsy to revoke the draft constitution, which is scheduled for a referendum mid-month, and a controversial decree granting himself increased powers.
Fighting quickly broke out when Morsy's Islamist supporters joined the ongoing demonstration Wednesday and vowed to stage a sit-in until the constitution is approved.
Physician Charles Hanna estimated that the makeshift clinic set up at the evangelical church near the protests had treated more than 40 injured protesters who sustained fractures, injuries from stone throwing and birdshot and deep cuts from knives.
"There were all kinds of arms used in this battle, very scary," he said, adding that the volunteer doctors treated the wounded from both sides.
"We have a precedent [for the church clinic]; a field hospital was also set up in the evangelical church in Qasr al-Dobara during clashes in Tahrir Square and doctors working there came and gave us tips."
After hours of violence subsided, traffic was moving through streets strewn with rocks. Some Morsy supporters remained in the area, huddling in blankets and reading the Quran, Reuters reported.
"We came here to support President Morsy and his decisions. He is the elected president of Egypt," Emad Abou Salem, 40, a Morsy supporter, told the news agency. "He has legitimacy and nobody else does."
Pro-Morsy protesters are manning checkpoints at the entrances to the streets leading to the palace to prevent opposition protesters who are now based in Roxy neighborhood from approaching, according to MENA.
Among the victims is 22-year-old Mohamed Mohamed al-Senousy, who died of a gunshot to the chest, according to the chief physician at the Mansheyet al-Bakry public hospital, Milad Ismail.
The field hospital also received in the early hours of Thursday the body of Hany Sanad al-Emam, 32, who had been shot in the chest with birdshot pellets, Ismail added.
The head of the ambulance authority, Mohamed Sultan, had earlier announced that three casualties had died of birdshot wounds: Mahmoud Mohamed Ibrahim, Mohamed Khelaf and Mohamed Mamdouh Ahmed.