First off: any meeting that lasts more than an hour (some would say 45 minutes) is poorly planned. I would NOT mention that to your boss. Try to generate an agenda for these calls so that you both can stay on topic rather than just jabbering for two hours.
Over the course of my career, I've frequently found myself offsetting my work day to more closely align with that of any remote teams or coworkers. At one job, I worked with a team with a seven hour time difference. Not impossible to handle, but if I had tried to plan a meeting in my afternoon (late at night for them), I probably would've been skewered. Suggesting an alternate time for the call is a good idea.
Since you're new in this position, I'd be very careful saying things like "I have to go at X time" to your boss, as this can come across as being lazy or uncommitted. A better solution may be to propose an alternate meeting time, perhaps an hour earlier than your current arrangement, and make sure you have an agenda ready. This is crucial to having brief, useful meetings.
Also, it's not clear from your post if these calls are scheduled, or if your manager just calls when it is convenient. If it's the former, proposing an alternate time is perfectly acceptable. If the latter, well, suggest to her that the call should be scheduled. If you're too uncomfortable to suggest this directly to her, create a meeting on your Outlook (or whatever) calendar, with yourself and your manager as the attendees. She can move it on her calendar or propose an alternate time.
Remember that managers have multiple employees, and typically also "real work" to handle in addition to managing. You'll probably be doing her a favor by setting expectations on times and duration. (ProTip: "setting expectations" is key to success in every career.)
This is as much her problem as it is yours. Part of being a manager, working with a geographically distributed team, is handling time differences. This has been a solved problem for decades. And, she may be as flustered as you are, but unaware of the difficulties it's causing.