[phenixbb] Two ions at same position
Nathaniel Echols
nechols at lbl.gov
Mon Aug 4 08:56:48 PDT 2014
On Sat, Aug 2, 2014 at 8:36 AM, Alastair Fyfe <afyfe at soe.ucsc.edu> wrote:
> I also ran into this recently and was puzzled about the correct PDB
> encoding. Using the same residue number with differing altloc, atom name
> and element fields seems straightforward but what should the residue name
> be ? In my experience not all PDB-processing software is happy with
> different residue names for the same residue number. Is there definitive
> PDB documentation for this case?
>
This does appear to be permitted by the PDB (in addition to Phenix, of
course) - a good example is crambin (1CBN), which has a naturally occurring
polymorphism:
ATOM 352 N ASER A 22 4.909 12.659 -3.127 0.20 3.03 N
ATOM 353 N BSER A 22 4.909 12.659 -3.127 0.20 3.03 N
ATOM 354 CA ASER A 22 6.035 13.459 -2.622 0.20 3.04 C
ATOM 355 CA BSER A 22 6.035 13.459 -2.622 0.20 3.04 C
ATOM 372 N CPRO A 22 4.909 12.659 -3.127 0.60 3.03 N
ATOM 373 CA CPRO A 22 6.035 13.459 -2.622 0.60 3.04 C
There are other examples of crambin that are numbered differently but
this is presumably due to the preferences of the investigator and/or
the limitations of the refinement software used. A counter-example is
3QXB, which has mixed metal sites:
HETATM 9585 FE A FE A 301 -6.546 23.487 57.436 0.66 26.72 FE
HETATM 9586 MN B MN A 302 -6.549 23.490 57.439 0.34 25.22 MN
I would say that if software can't handle the first case (same residue
number, different residue name) that is a bug, but there doesn't
appear to be consensus on the "correct" way to do things. My
preference would be to keep the numbering the same but the PDB will
accept either convention.
-Nat
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