I will have about 7 hours transit at Istanbul Ataturk and my first flight will arrive there at 04:45 am. Will the transit be open at this time ? In other words, can I directly go to transit or should I wait outside the transit until it will be opened ?
Istanbul Ataturk airport is open 24 hours. I have personally gone through transfer in the international zone at 4 or 5 in the morning several times. I believe the domestic zone is the same. Note that the gate information likely won't be available until about two hours before departure of your second flight.
Please edit your question and add details of your flights (from/to locations, times, airlines, whether they are all on one ticket or separate tickets) - and we might be able to help further.