You could use one of the simple Discovery studio visualiser, Pymol or even VMD to combine/merge your pdb files. However, few of the following things to be considered before you merge:

(i) coordinates should not overlap or else you would not get a proper pdb

(ii) You could place your DNA nearby your crystal structure according to your desired site and then can manually rotate/move unless you see a suitable structure. Some small overlaps can be removed with a small geometry optimisation.

(iii) Ions can be placed as described in (i) or packmol can be useful. However, that would probably increase your efforts.

Hope that helps you in a way. I am sure others will responds who might provide an easy way for you.

In which form do you have the coordinates now? Most visualization programs will allow you to save the coordinates of multiple objects into a single pdb file at their current relative orientation, e.g. in PyMOL:

save myFile.pdb, (obj1 or obj2 or obj3 or obj4)

If you have multiple objects as separate pdb file in correct relative orientation, you can also just use a text editor to copy the coordinate section into one file.

However, you want to make sure that the different parts combined into one file have different chain labels, as ambiguous chain/residue label may cause problems in future processing of your pdb file.

Thank you for your grate answers.

Use Chimera...

Pathway:

Tool --> Structure comparison --> Match and Align --> save PDB

Good luck