from decimal import Decimal

'%.2E' % Decimal('40800000000.00000000000000')

# returns '4.08E+10'

In your '40800000000.00000000000000' there are many more significant zeros that have the same meaning as any other digit. That's why you have to tell explicitly where you want to stop.

If you want to remove all trailing zeros automatically, you can try:

def format_e(n):
    a = '%E' % n
    return a.split('E')[0].rstrip('0').rstrip('.') + 'E' + a.split('E')[1]

format_e(Decimal('40800000000.00000000000000'))
# '4.08E+10'

format_e(Decimal('40000000000.00000000000000'))
# '4E+10'

format_e(Decimal('40812300000.00000000000000'))
# '4.08123E+10'