try this, may work for you.
UPDATE runquery.table1
SET runquery.table1.`Column1` = (select (runquery.table2.`Col1`/runquery.table2.`Col2`*100) from runquery.table1 , runquery.table2 WHERE runquery.table2.`itemid` = 3 AND runquery.table1.`Userids` = runquery.table2.`userid`, runquery.table1.`Column2` = select (runquery.table2.`Col1`/runquery.table2.`Col2`*100) from runquery.table1 , runquery.table2 WHERE runquery.table2.`itemid` = 5 AND runquery.table1.`Userids` = runquery.table2.`userid`;