All I can say is to call the mobo maker and ask them, it may be backward compatable and run at x16 on one of the x32 slots. Or you can just try it out. What in the world are you building anyways?? That is one heck of a board! The card you have is recommended with this board Gigabyte K8NXP-SLI
This board is equipped with the x16 pci-x card as well as the x1 pci-x and standard pci slot. Hopefully they will be of some help to you, wish I could help you more but I have never seen such a beefy mobo before.