You enter the 1099-R exactly as it is. Form 5498 is information only.
Federal tax withholding is money that is withheld from the distribution, not something that is paid to you. Possibly they withheld too much and returned the difference to you. If that is the case and they did not actually withhold the box 4 amount then they should have issued a corrected 1099-R. You should contact the payer to be sure.
If this was done in 2017, then it will probably be reported on your 2017 1099-R.