Removing a database will delete that database from it's online location. Be sure that you have saved a copy of the database if you want to keep any of the information in the database. Removing a database will not remove any user's but it will remove all user's permissions to that database.
To remove a database:
Click on the Add/Remove MySQL Databases link in the Domain Menu area.
Click on the 
button next to the specific database in the Existing MySQL databases area. Click on the MySQL databases link to return to the MySQL databases window to confirm that the database has been removed.