Atom Nomenclature for JGD

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 JGD

Atom Name (V3) Atom Name (V2)
C01 C1
N02 N1
C03 C2
C04 C3
C05 C4
C06 C5
N07 N2
C08 C6
C09 C7
H011 H1
H012 H2
H013 H3
H032 H4
H033 H5
H031 H6
H051 H7
H061 H8
H081 H9
H091 H10