You should be OK installing NE over that version but I'd suggest you do a full backup of the /opt/zimbra directory first, you can use one of the scripts from
these articles. You'll need to upgrade to 4.5.11 before you move to the 5.0.x version, when you've done the first upgrade make sure that the systems works OK then perform another full backup and do the 5.0.x upgrade. Again, make sure everything's working OK on this server before you move to the new server. You said it's Ubuntu 6, is it the Ubuntu 6.06 LTS version?
Just in case you have problems and need to restore., do you still have the original install files for the version of Zimbra that you're running? One of the articles in the link above describes how to move from one server to another, have a read of that (and search the forums) to make sure you understand what's needed before you do the move. Any questions, please ask.