Graphics Card and Motherboard Problem...

So basically, I own a HP Media Center PC m1264n, which isn't meant for gaming, but it can run Call of Duty and Command and Conquer Generals at maximum graphics settings, so I figured it could handle Call of Duty 2, Battlefield 2 and F.E.A.R. I bought them, and they won’t even run. I kept getting DirectX errors. After asking around online and contacted HP support, they all said that the Intel 910GL integrated video card was too weak to handle them, so I had to get a new graphics card. I bought and Nvidia FX6600. However, Nvidia FX6600 is a PCI-e graphics card, and my computer only has PCI slots. I thought PCI-e and PCI were the same, but my 6600 won’t fit in my PCI slot. I realize I may need to purchase a new motherboard, one with PCI-e slots. Is it safe to replace a desktop's motherboard? If so, can you recomend any specific models?