Essentially, what you are most concerned about is that your slot is PCIe x16, to match the physical connection on the graphics card. The card can be designed to work with the PCIe version 1, 2, or even 3 standard, and if your slot is only designed to run the PCIe version 1 standard, the graphics card will simply, and without you having to tell it to, run at PCIe version 1 signaling.
You will lose some bandwidth between the graphics card and the rest of the computer, but the only alternative to that would be to upgrade the motherboard to something with PCIe version 2 or newer.
On the whole, you probably won't notice much of a speed difference from running the card at PCIe v.1