Do I enter IRA contributions in W2 box 12a code D (with Retirement plan checked in box 13) when asked for total contributions made in 2016?

I made a $1,560 IRA contribution via payroll deduction.  It is shown on my W2 in box 12a with code 'D', and retirement plan is checked in box 13.  I contributed $5,500 directly to a different IRA.  When Turbotax asks for contribution made to IRA in 2016, do I add these 2 amounts together or is the one shown on W2 with Retirement plan checked in box 13 handled differently?