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Habibur Rehman Sheikh (28) alias Habibur or Sheikh was apprehended by the central agency from the Dodabalpur area of the city, they said.
Sheikh was named in the charge sheet filed by the NIA in this case in March 2015 “for his direct involvement in the conspiracy of JMB to wage war against governments of India and Bangladesh”, an NIA official said.
He was a close associate of senior JMB leader Jahidul Islam alias Kausar and was associated with other JMB leaders like Rahamatullah Sheikh and Moulana Yusuf, the official said.
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He was produced on Tuesday before a special NIA court in Bengaluru which granted the agency five-day transit remand for further production before a court in Kolkata.
Two persons were killed and another was injured in a bomb explosion at a house in the Khagragarh locality of Burdwan on October 2, 2014.
The outfit was banned by the Bangladesh government in 2005, while India banned it this year in May.
In a notification, the home ministry had said the outfit has committed and promoted acts of terrorism and has been engaged in radicalisation and recruitment of youths for terrorist activities in India.