While correct that it will not work at x16, it's still a reasonable idea to try the x8 or x4 slot, and do a benchmark test.
Unless you have a top of the line card, it's very unlikely that the graphics card needs all the bandwidth of x16.
You might find that at x4 or x8 (if you can use the second last slot), depending on your configuration, graphics card, and games etc, you might not have any real world impact by stepping down in bus bandwidth.
I'd try both a synthetic test, such as unigene, as well as a couple of games.
It will also depend on whether your graphics card is PCIE 2 or 3, as that changes the bandwidth available at any x speed. (i.e. PCIE 2.0 x16 is slower than PCIE 3.0 x16)