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Card you provided use PCIe v1.0 interface. So you can use any free slot. Also there is no benefit to put it in v2.0 slot.

P.S. Your Mac Pro slot configuration
Mac Pro 3,1 (2008):

  • Slot 1: PCIe v2.0
  • Slot 2: PCIe v2.0
  • Slot 3: PCIe v1.0
  • Slot 4: PCIe v1.0
 
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