The legacy PDB format has a field called “altLoc” (alternate location indicator) for "ATOM/HETATM" records in the "Coordinate Section". The corresponding documentation is excerpted below:
COLUMNS DATA TYPE FIELD DEFINITION
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17 Character altLoc Alternate location indicator.
AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples).
- For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:
- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.
In mmCIF format, AltLoc is under the atom_site category, with attribute name label_alt_id: i.e., labelled as _atom_site.label_alt_id. It is a required data item and appears in 43% of entries in the PDB.
In 3DNA and DSSR, AltLoc has a default value of "A1 ": an atom is taken into consideration if its AltLoc field (a single character) is space, A, or 1, otherwise it is ignored. Note that for mmCIF format, AltLoc field with dot (.) or question mark (?) is taken as space. Customized AltLoc values can be set via the --altloc option in DSSR.
Here is an example. PDB entry 7o1h is a 31-mer synthetic construct, with a hybrid-2R quadruplex-duplex of 3(-P-P-Lw) topology and three syn guanosines. It contains two modified residues designated BGM (BGM26 and BGM28), 8-bromo-2'-deoxyguanosine-5'-monophosphate, with AltLoc set to B. By default, DSSR detects only one G-tetrad, consisting of DG5,DG9,DG13,DG27, ignoring the two G-tetrads with BGM26 and BGM28. With the --altloc=B option (space is always included), all three G-tetrads are detected and the G-quadruplex (a G4-stem) is then automatically annotated as 3(-P-P-Lw):
# x3dna-dssr -i=7o1h-assembly1.cif --altloc=B
List of 2 types of 3 modified nucleotides
nt count list
1 BGM-g 2 A.BGM26,A.BGM28
2 THM-t 1 A.THM1
List of 1 G4-stem
Note: a G4-stem is defined as a G4-helix with backbone connectivity.
Bulges are also allowed along each of the four strands.
stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(-P-P-Lw) note=hybrid-2R(3+1) UUUD hybrid-(mixed)
1 glyco-bond=---s sugar=---. groove=--wn WC-->Major nts=4 GGGg A.DG4,A.DG8,A.DG12,A.BGM28
2 glyco-bond=---s sugar=--.- groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG27
3 glyco-bond=---s sugar=---- groove=--wn WC-->Major nts=4 GGGg A.DG6,A.DG10,A.DG14,A.BGM26
step#1 pm(>>,forward) area=13.57 rise=3.39 twist=26.7
step#2 pm(>>,forward) area=12.00 rise=3.44 twist=28.4
strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG4,A.DG5,A.DG6
strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
strand#3 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG12,A.DG13,A.DG14
strand#4 D DNA glyco-bond=sss sugar=.-- nts=3 gGg A.BGM28,A.DG27,A.BGM26
loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT11
loop#3 type=lateral strands=[#3,#4] nts=11 ACGCGCAGCGT A.DA15,A.DC16,A.DG17,A.DC18,A.DG19,A.DC20,A.DA21,A.DG22,A.DC23,A.DG24,A.DT25See G4.x3dna.org for DSSR-enabled annotation and visualization of this G4 structure. Here is the G4-stem in the frame of reference of 5' DG4 (bottom right), following the convention of Dvorkin et al. (2018). It is orientated automatically based on the standard base-reference frame (Olson et al. (2001)) of DG4.
References:
- Dvorkin, Scarlett A., Andreas I. Karsisiotis, and Mateus Webba Da Silva. 2018. “Encoding Canonical DNA Quadruplex Structure.” Science Advances 4 (8): eaat3007. https://doi.org/10.1126/sciadv.aat3007.
- Olson, Wilma K, Manju Bansal, Stephen K Burley, Richard E Dickerson, Mark Gerstein, Stephen C Harvey, Udo Heinemann, et al. 2001. “A Standard Reference Frame for the Description of Nucleic Acid Base-Pair Geometry.” Journal of Molecular Biology 313 (1): 229–37. https://doi.org/10.1006/jmbi.2001.4987.
