The video card would most likely be at the bottom of the 5.25" drive bays, so if it's empty, it would fit right in there.
+1
HOWEVER, better check your MB setup. I built a system and the card I went with took up 2 PCI slots because of it's thickness, so it was critical that the GPU card socket lined up properly (it did). This should not be an issue, but when mounting the MB into your new case, be certain that the GPU socket lines up so you get that longer space for the card. Most cases allow you to mount a MB in more than just one position, but you won't know until you put it together.