When you receive Form 1099-S, you must enter the gross amount shown in Box 2 as "net proceeds" (this field name is a quirk in that section of TurboTax).
Be sure to check the box for "I have selling expenses not reported..." in order to enter all your selling expenses (see screenshot below - click to enlarge).
Also, click the box for "Income taxes were withheld for this sale" to reveal the drop-down boxes for Federal and State taxes you've already paid.
You may have received far less cash from the sale because mortgage payoffs, property taxes, and other pro-rated or loan-related costs are not deducted when calculating gross proceeds.
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