Hi Pajamurai, welcome to BC.

QUOTE
The part I'm talking about is the little purple and green holes that the mouse and keyboard can go into.
Those are your PS2 ports. You cannot "take those out" unless you want a dead computer.
If the card will not fit properly in any slot configuration, buy one that will.
If you post make and model of computer and the graphics card you're trying to install, we can be of much more help.