On our old shared/sdx/reseller servers, we have setup 4.1.x which is still the most popular version and is supported by most web applications. Unfortunately we can not upgrade this to 5.x as this will break a lot of customer’s websites.
On the other hand our new shared/sdx/reseller servers are setup with MySQL 5.0.x.
If you need to use newer version i.e. 5.x, you can ask JaguarPC Support to move your account to the newer server but make sure the queries in your scripts/applications are compatible with 5.x version.