Zvezda, the third ISS module, (I think it was Zarya (FGB), Node 1, and then Zvezda) known as the Service Module was actually built as a spare for Mir and was originally to be the core of Mir-2. But with the merging of the US and Russian station plans, it became the key building block of the initial ISS.
As a Mir spare, the docking module had 5 ports. 6 if you count its connection to the Service Module itself. As delivered to the ISS it only has nadir (Earth facing) and zenith (space facing) ports, and of course the port it uses to dock to Zarya.
Why did they remove two docking ports? It seems like the flexibility would have been useful, and it was already built that way.