It could if the x1 pcie slot is is shared with either of the x16 slots in use. Check your owners manual.
* It looks like the black pcie x16 slot drops to a x1 mode if there is a card in the second pcei2.0 x16 slot. Your manual is confusing on this because the graphic right above it says x4 or x1 if the other two slots are occupied. Looks like you'll be ok as long as you drop that new card into one of the x1 lsots.