What's your exact motherboard model and complete system specs? There have been 3 generations of PCI-E. You may very well have problems if you're trying to use a new graphics card on a PCI-E 1.0 motherboard.
PCIe 3.0 is backwards compatible all the way to 1.0. That specific card would only really see a performance impact if it were a 1.0 slot, and it was operating in x8 mode. If that's the case, the CPU would be ancient (from the pre-Core Duo era), and would end up being the bottleneck.
Regardless, the card will work in a single x16 slot, regardless of what kind of slot it is. Older versions might not perform as well as newer slots, but with that card, it's extremely unlikely that it will be an issue.