This is internal view of my Storm Case iM2500.
As you can see the hole in lid, penta-prism will fit in this area.
Here is the list of equipments in the case.

Nikon D2x
AF-S DX Nikkor 17-55mm F2.8G
AF-S VR Nikkor 70-200mm F2.8G
AF-S DX Nikkor 12-24mm F4G
Ai AF Nikkor 50mm F1.4D
Ai AF Nikkor 85mm F1.4D
SB-800
x1.4 and x1.7 Teleconverter
Circular Polarizer (77mm)
Closeup filter (f=500mm 77mm)
Cable Release