Where are the Hydrogen Atoms?
Most crystallographic experiments do not resolve hydrogen atoms, so most of the crystallographic coordinate files in the PDB archive only include positions for the non-hydrogen atoms. In some cases, the polar hydrogen atoms are included (polar hydrogen atoms are those that are attached to nitrogen, oxygen and sulfur, which can participate in hydrogen bonds) when they are used during the refinement of the structure. NMR-determined structures, on the other hand, most often include all of the hydrogen atoms in the structure, since much of the experimental information obtained in these experiments consists of the distance between these hydrogen atoms. Since crystallographic experiments typically do not see hydrogen atoms, and since oxygen and nitrogen atoms have similar numbers of electrons and thus look similar in crystallographic electron density maps, it is often difficult to determine the exact identity of atoms in sidechains such as asparagines and glutamines. In some cases, if you lo
