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Faruk Koca has resigned as president of Ankaragucu after punching a referee at the end of a Super Lig match on Monday night.
Matches in all Turkish football leagues were suspended indefinitely by the country's football association after Koca ran onto the pitch and struck official Halil Umut Meler following their top-flight game against Rizespor.
On Tuesday, a Turkish court ordered the arrest of Koca and also remanded in custody two other suspects over the violence, the justice minister Yilmaz Tunc revealed.
Tunc said Koca and two others were formally arrested for "injuring a public official" after prosecutors took statements from them.
In a letter confirming his resignation, Koca wrote: "After the match we played against Çaykur Rizespor last night, due to my attitude towards the referee Halil Umut Meler, who managed the match, Mr. Meler and his family, in particular; I apologise to the Turkish referee community, sports public and our nation.
"How and why the subject came to this point is independent of the event. No matter how great injustice or wrong it is, nothing can legitimise or explain the violence that I committed, which I definitely did not desire.
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