Recently, I came across and was a bit surprised by the different assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format. Using PDB entry 1ehz (the crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution) as an example, 1MA58 in .pdb has atomic coordinates listed as:
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 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 and the corresponding section in .cif 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 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 checked exhaustively, the same inconsistency also occurs in several other cases I tested (e.g., 1s72, the Haloarcula Marismortui large ribosomal subunit). Has anyone on this list experienced similar issue? Thanks, -- Xiang-Jun PS. This is a slightly revised message initially sent to pd...@sdsc.edu on Friday, May 22. Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/
