If you have the "slimline" version, then no. What specific s3000 (look on the tag on the back or bottom) model do you have?
Also, even if a microATX motherboard will fit, you will likely have to modify your HP's front panel connectors (power, reset, HD LED, power LED) to connect to a standard motherboard. Not a big deal, but something to consider.
Last, depending on the actual model you have, you may also have an issue with your power supply (PSU) and whether, or not, it can power your intended new configuration.