Can I install a single GPU on PCI-e slot #2?

[thupple]

MOBO = ASUS P877-V Premium
http://www.asus.com/Motherboards/Intel_Socket_1155/P8Z77V_PREMIUM/#specifications

GPU = ASUS GTX 680
http://www.asus.com/Graphics_Cards/NVIDIA_Series/GTX680DC2O2GD5/#specifications

The GPU is hugemongus. It takes up three slots.

I have a CPU Cooler = http://www.antec.com/Believe_it/product.php?id=Mjc2OA==&lan=us
But it won't fit if I put the GPU in PCI-e Slot 1

What are the consequences if I put the GPU in Slot2?

I'd rather just get a new CPU Cooler than sacrifice performance..but not sure if that is the case.

Thanks in advance for your input.

 

[Deemo13]

I run my GPU in slot 2. Its not a huge deal. Just moves the GPU down.