One of the most important things for your web site is the Database. It is necessary to take the backup of your web site as well as Databases on regular basis. One of the easy sway to take backup of your MySQL database is via cron. And then you can download the backup via FTP. you can set the below cron to take MySQL backup on daily basis:
0 * * * * /usr/bin/mysqldump -u databaseusername databasename -ppassword > /path/to/take/backup.sql
The above cron will dump your MySQL database at 12 (Mid night) each day. You can set the cron time based on your convenient time.