The 3.0 / 2.1 / 2.0 is the version of the PCI-e thats given by the motherboard chipset.
The x16 x8 ... x1 specification is the lenght and bandwidth of the slot or card.
So you can't compare apples to oranges. However a 16x PCI-e Graphics card thats rated at PCI-e 3.0 can run on any x16 slot even if its 1.0/2.0 etc.
So to sum up : x16 (full length) graphics card can run only on x16 slot on the motherboard but versions don;t matter - 3.0 card runs on 1.0 slot and viceversa