Thats unusual as most case LED leads I have seen have always been two pins.
You may need to do a bit of bodging to overcome it.
One way that comes to mind, if you have a couple of jumpers off an old hard drive or CD drive, is to place one side of each jumper over one pin on the mobo then using two short pieces of wire of the right thickness (a bit of fuse wire or the copper earth wire from mains cable twin and earth) to connect to the case LED plug.