Assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format

Recently, I came across and have been surprised by the different assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format. As always, the issue is best illustrated with a concrete example. Here is what I observed in the PDB entry 1ehz, the crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution.

DSSR identifies 14 modified nucleotides (of 11 types) in 1ehz as shown below:

List of 11 types of 14 modified nucleotides
      nt    count  list
   1 1MA-a    1    A.1MA58
   2 2MG-g    1    A.2MG10
   3 5MC-c    2    A.5MC40,A.5MC49
   4 5MU-t    1    A.5MU54
   5 7MG-g    1    A.7MG46
   6 H2U-u    2    A.H2U16,A.H2U17
   7 M2G-g    1    A.M2G26
   8 OMC-c    1    A.OMC32
   9 OMG-g    1    A.OMG34
  10 PSU-P    2    A.PSU39,A.PSU55
  11 YYG-g    1    A.YYG37

In file 1ehz.pdb downloaded from RCSB PDB, all the 14 modified nucleotides are assigned as HETATM whereas in 1ehz.cif the corresponding records are ATOM. Here is the excerpt for 1MA58 in PDB format:

HETATM 1252  P   1MA A  58      73.770  67.765  34.057  1.00 30.65           P  
HETATM 1253  OP1 1MA A  58      72.638  67.886  33.105  1.00 32.84           O  
HETATM 1254  OP2 1MA A  58      73.621  68.229  35.450  1.00 29.49           O  
HETATM 1255  O5' 1MA A  58      74.315  66.273  34.254  1.00 28.81           O  
HETATM 1256  C5' 1MA A  58      74.592  65.439  33.080  1.00 29.42           C  
HETATM 1257  C4' 1MA A  58      74.279  63.972  33.383  1.00 33.42           C  
HETATM 1258  O4' 1MA A  58      74.880  63.685  34.667  1.00 32.36           O  
HETATM 1259  C3' 1MA A  58      72.789  63.573  33.509  1.00 35.13           C  
HETATM 1260  O3' 1MA A  58      72.625  62.168  33.250  1.00 36.80           O  
HETATM 1261  C2' 1MA A  58      72.560  63.667  35.012  1.00 34.80           C  
HETATM 1262  O2' 1MA A  58      71.525  62.828  35.506  1.00 36.27           O  
HETATM 1263  C1' 1MA A  58      73.908  63.150  35.551  1.00 33.62           C  
HETATM 1264  N9  1MA A  58      74.284  63.494  36.930  1.00 30.36           N  
HETATM 1265  C8  1MA A  58      73.887  64.574  37.688  1.00 34.55           C  
HETATM 1266  N7  1MA A  58      74.415  64.610  38.899  1.00 33.32           N  
HETATM 1267  C5  1MA A  58      75.204  63.469  38.953  1.00 33.37           C  
HETATM 1268  C6  1MA A  58      76.031  62.941  39.948  1.00 33.58           C  
HETATM 1269  N6  1MA A  58      76.184  63.488  41.134  1.00 41.19           N  
HETATM 1270  N1  1MA A  58      76.708  61.803  39.669  1.00 34.48           N  
HETATM 1271  CM1 1MA A  58      77.649  61.222  40.626  1.00 31.43           C  
HETATM 1272  C2  1MA A  58      76.527  61.216  38.479  1.00 28.43           C  
HETATM 1273  N3  1MA A  58      75.793  61.624  37.453  1.00 31.67           N  
HETATM 1274  C4  1MA A  58      75.142  62.771  37.747  1.00 33.02           C  

The corresponding section in PDBx/mmCIF format is:

ATOM   1252 P  P     . 1MA A 1 58 ? 73.770 67.765 34.057  1.00 30.65  ? ? ? ? ? ? 58  1MA A P     1 
ATOM   1253 O  OP1   . 1MA A 1 58 ? 72.638 67.886 33.105  1.00 32.84  ? ? ? ? ? ? 58  1MA A OP1   1 
ATOM   1254 O  OP2   . 1MA A 1 58 ? 73.621 68.229 35.450  1.00 29.49  ? ? ? ? ? ? 58  1MA A OP2   1 
ATOM   1255 O  "O5'" . 1MA A 1 58 ? 74.315 66.273 34.254  1.00 28.81  ? ? ? ? ? ? 58  1MA A "O5'" 1 
ATOM   1256 C  "C5'" . 1MA A 1 58 ? 74.592 65.439 33.080  1.00 29.42  ? ? ? ? ? ? 58  1MA A "C5'" 1 
ATOM   1257 C  "C4'" . 1MA A 1 58 ? 74.279 63.972 33.383  1.00 33.42  ? ? ? ? ? ? 58  1MA A "C4'" 1 
ATOM   1258 O  "O4'" . 1MA A 1 58 ? 74.880 63.685 34.667  1.00 32.36  ? ? ? ? ? ? 58  1MA A "O4'" 1 
ATOM   1259 C  "C3'" . 1MA A 1 58 ? 72.789 63.573 33.509  1.00 35.13  ? ? ? ? ? ? 58  1MA A "C3'" 1 
ATOM   1260 O  "O3'" . 1MA A 1 58 ? 72.625 62.168 33.250  1.00 36.80  ? ? ? ? ? ? 58  1MA A "O3'" 1 
ATOM   1261 C  "C2'" . 1MA A 1 58 ? 72.560 63.667 35.012  1.00 34.80  ? ? ? ? ? ? 58  1MA A "C2'" 1 
ATOM   1262 O  "O2'" . 1MA A 1 58 ? 71.525 62.828 35.506  1.00 36.27  ? ? ? ? ? ? 58  1MA A "O2'" 1 
ATOM   1263 C  "C1'" . 1MA A 1 58 ? 73.908 63.150 35.551  1.00 33.62  ? ? ? ? ? ? 58  1MA A "C1'" 1 
ATOM   1264 N  N9    . 1MA A 1 58 ? 74.284 63.494 36.930  1.00 30.36  ? ? ? ? ? ? 58  1MA A N9    1 
ATOM   1265 C  C8    . 1MA A 1 58 ? 73.887 64.574 37.688  1.00 34.55  ? ? ? ? ? ? 58  1MA A C8    1 
ATOM   1266 N  N7    . 1MA A 1 58 ? 74.415 64.610 38.899  1.00 33.32  ? ? ? ? ? ? 58  1MA A N7    1 
ATOM   1267 C  C5    . 1MA A 1 58 ? 75.204 63.469 38.953  1.00 33.37  ? ? ? ? ? ? 58  1MA A C5    1 
ATOM   1268 C  C6    . 1MA A 1 58 ? 76.031 62.941 39.948  1.00 33.58  ? ? ? ? ? ? 58  1MA A C6    1 
ATOM   1269 N  N6    . 1MA A 1 58 ? 76.184 63.488 41.134  1.00 41.19  ? ? ? ? ? ? 58  1MA A N6    1 
ATOM   1270 N  N1    . 1MA A 1 58 ? 76.708 61.803 39.669  1.00 34.48  ? ? ? ? ? ? 58  1MA A N1    1 
ATOM   1271 C  CM1   . 1MA A 1 58 ? 77.649 61.222 40.626  1.00 31.43  ? ? ? ? ? ? 58  1MA A CM1   1 
ATOM   1272 C  C2    . 1MA A 1 58 ? 76.527 61.216 38.479  1.00 28.43  ? ? ? ? ? ? 58  1MA A C2    1 
ATOM   1273 N  N3    . 1MA A 1 58 ? 75.793 61.624 37.453  1.00 31.67  ? ? ? ? ? ? 58  1MA A N3    1 
ATOM   1274 C  C4    . 1MA A 1 58 ? 75.142 62.771 37.747  1.00 33.02  ? ? ? ? ? ? 58  1MA A C4    1 

While I have not tested exhaustively, it seems true that PDBx/mmCIF has adopted a different definition of what constitutes a HETATM residue. It is worth noting that results from 3DNA and DSSR/SNAP are not effected by the conflicting assignments.

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