For any credit card transaction, there are charges which the credit card service provider charges. However, we see no such provision to include those charges in credit card transactions.
All credit card transaction amounts go to Undeposited Funds account. Now when we choose to deposit those funds to the bank, in that deposit sheet, there must be a field for the related charges (and the vat on those charges) .

So the the amount which is deposited in the bank matches the actual amount which is credited in the actual bank.