Why there is an alternate location indicator (position 17) in PDB file?

Question

[ganuongphap]

Like this:

HETATM 1519  C1 AAB1 B 100     -12.826  12.835  34.863  0.50 14.18           C
HETATM 1520  C1 BAB1 B 100       -4.549  17.796  20.909  0.50 14.18           C
________________^

There is only one C1 atom in AB1, but now we have the A and B version of this. I guess that because of the X-ray crystallography method, which has diffraction. But I am not sure about that.

Answer 1

[João Rodrigues]

When interpreting the x-ray diffraction and its correspondent electron density map, sometimes the position the a particular atoms is not crystal clear (pun intended). The atom can be too mobile, the density particularly bad at in that region, etc.. it's also tied to the occupancy factor (the second to last column, 0.50 in your example) which is 1.00 if the atom is observed 100% of the time at one place, less if split between different locations. In these cases, you have multiple entries per location of the same atom, differentiated by the character at position 17.