Atom Nomenclature for 004

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 004

Atom Name (V3) Atom Name (V2)
C C
N N
O O
CA CA
CB CB
CE CE
CD1 CD1
CD2 CD2
CG1 CG1
CG2 CG2
OXT OXT
H HN
H2 HNA
HA HA
HE HE
HD1 HD1
HD2 HD2
HG1 HG1
HG2 HG2
HXT HXT