What do these characters mean in a PDB file?

Question

The 33rd atom information in 3nir.pdb is written as follows:

ATOM 33 N ATHR A 2 4.935 -11.632 15.046 0.74 2.95 N

How should I interpret N A in the above line?

I mean, what does it mean? Is it Sodium or Nitrogen?

If it is Nitrogen, what does A mean then?

Answer 1

from https://www.wwpdb.org/documentation/file-format

Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.30 Document Published by the wwPDB This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html. I believe PDB format is kind of outdated, but not sure..

At page 177 it says about altLoc:

• 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.

your question could be more useful if you post the entire description for residue 2:

ATOM     33  N  ATHR A   2       4.935 -11.632  15.046  0.74  2.95           N
ATOM     34  N  BTHR A   2       5.078 -11.406  15.180  0.31  2.78           N  
ATOM     35  CA ATHR A   2       5.757 -11.521  13.850  0.81  3.02           C  
ATOM     36  CA BTHR A   2       5.773 -11.153  13.921  0.20  2.67           C  
ATOM     37  C  ATHR A   2       7.070 -10.839  14.210  0.74  2.82           C  
ATOM     38  C  BTHR A   2       7.155 -10.559  14.193  0.29  1.80           C  
ATOM     39  O  ATHR A   2       7.152  -9.941  15.050  0.80  3.31           O  
ATOM     40  O  BTHR A   2       7.214  -9.641  15.012  0.25  2.41           O  
ATOM     41  CB ATHR A   2       4.976 -10.693  12.813  0.87  5.53           C  
ATOM     42  CB BTHR A   2       4.896 -10.354  12.941  0.25 12.07           C  
ATOM     43  OG1ATHR A   2       4.611  -9.432  13.388  1.00  6.88           O  
ATOM     44  OG1BTHR A   2       3.743 -11.083  12.501  0.25  9.57           O  
ATOM     45  CG2ATHR A   2       3.858 -11.584  12.293  0.75 10.03           C  
ATOM     46  CG2BTHR A   2       5.683  -9.885  11.726  0.27  5.90           C  
ATOM     47  H  ATHR A   2       4.547 -10.814  15.527  0.75  3.44           H  
ATOM     48  H  BTHR A   2       5.510 -10.211  15.754  0.25  2.90           H  
ATOM     49  HA ATHR A   2       5.962 -12.339  13.548  0.75  3.32           H  
ATOM     50  HA BTHR A   2       4.036  -9.929  13.477  0.25  2.86           H  
ATOM     51  HB ATHR A   2       5.648 -10.589  11.938  0.75  5.43           H  
ATOM     52  HB BTHR A   2       4.644  -9.326  13.574  0.25  5.67           H  
ATOM     53  HG1ATHR A   2       5.030  -9.344  14.216  0.75  8.74           H  
ATOM     54  HG1BTHR A   2       3.236 -11.198  13.399  0.25 10.21           H  
ATOM     55 HG21ATHR A   2       4.096 -12.441  11.924  0.75 10.92           H  
ATOM     56 HG21BTHR A   2       6.542  -9.278  12.024  0.25  9.66           H  
ATOM     57 HG22ATHR A   2       3.222 -10.974  11.650  0.75 10.92           H  
ATOM     58 HG22BTHR A   2       5.039  -9.142  11.179  0.25  9.66           H  
ATOM     59 HG23ATHR A   2       3.163 -11.738  13.200  0.75 10.92           H  
ATOM     60 HG23BTHR A   2       5.904 -10.639  11.169  0.25  9.66           H