The black cylindrical thing is a capacitor.
Your graphics card will go in the black slot. You have to lock the card in place with the white clip. That clip when locked is higher than the capacitor. So I don't think there will be a problem. On some motherboards the graphics card extends over the SATA connectors.
You can use Google to search for pictures of an 3870/3850. On some pictures you can see that the card doesn't touch any components on the motherboard.