To upgrade the MySQL version to MySQL 4.1.16 in DirectAdmin, you need to create a script lets say, myup.sh and paste the following in it
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#!/bin/sh
/etc/rc.d/init.d/mysqld stop
cd $HOME
echo -e "\n\n\033[1;37web4host.net\033[0m\n\n";
wget
http://dev.mysql.com/get/Downloads/M.../mysql.he.net/
wget
http://dev.mysql.com/get/Downloads/M.../mysql.he.net/
wget
http://dev.mysql.com/get/Downloads/M.../mysql.he.net/
rpm -Uvh ./MySQL-server-4.1.16-1.i386.rpm
rpm -Uvh ./MySQL-client-4.1.16-1.i386.rpm
rpm -Uvh ./MySQL-devel-4.1.16-1.i386.rpm
rm -fr ./MySQL-server-4.1.16-1.i386.rpm ./MySQL-client-4.1.16-1.i386.rpm ./MySQL-devel-4.1.16-1.i386.rpm
echo -e "\n\n\033[1;37web4host.net\033[0m\n\n";
rm -f /etc/init.d/mysql
rm -f /etc/rc?.d/*mysql
/etc/rc.d/init.d/mysqld restart
exit 0;