this is the link to PDB file I am interested in
If you only want to find pair of atoms that are explicitly listed in the file (i.e. if you want to ignore symmetry operators -- a LYS residue could be far from a particular O5' atom in the same asu, but close to its symmetric image) then it's simple. But in general, if you want to account for crystal symmetry, I don't think that Biopython can help.
you could also install VMD....load the file....make the selection of what you want to keep.... write a new pdb