Atom Nomenclature for TRO

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for TRO

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
CG CG
CD1 CD1
OD1 OD1
NE1 NE1
CE2 CE2
CZ2 CZ2
CH2 CH2
CZ3 CZ3
CE3 CE3
CD2 CD2
C C
O O
OXT OXT
H H
H2 HN2
HA HA
HB2 1HB
HB3 2HB
HD1 HOD
HE1 HE1
HZ2 HZ2
HH2 HH2
HZ3 HZ3
HE3 HE3
HXT HXT