$string='ATOM   3316  N   TYR D  24      97.479  18.805   2.990  1.00 36.32      D    N 
ATOM   3322  CD1 TYR D  24      96.225  15.974   2.812  1.00 17.96      D    C';

$string=~s#((\w+)   \d{4}  \w   TYR )D#$1X#gsi;

print $string;

output:
*******
ATOM   3316  N   TYR X  24      97.479  18.805   2.990  1.00 36.32      D    N
ATOM   3322  CD1 TYR D  24      96.225  15.974   2.812  1.00 17.96      D    C