You don't need to iterate the array. Just:
>>> x = ['[email protected]', '[email protected]']
>>> x
['[email protected]', '[email protected]']
>>> x.remove('[email protected]')
>>> x
['[email protected]']
This will remove the first occurence that matches the string.
EDIT: After your edit, you still don't need to iterate over. Just do:
index = initial_list.index(item1)
del initial_list[index]
del other_list[index]