It will work just fine.
Just not up to it's potential.
EDIT: Looked at another thread, found this
Incorrect, there is no speed difference between 2.0 and 2.1. PCI-e 2.1 adds the new management features for PCI-e which will be used mostly in the 3.0 cards (whenever that standard is released) but there is no difference in speed between the two types. There is however a difference in speed between 1.0 and 2.0 and a medium to high end graphics card used on PCI-e 1.0 will encounter a throughput bottleneck.
Either way, I know it will work for sure. As long as it is a PCI-E slot, you will have no problems......which it is.....so you won't.