Atom Nomenclature for GOX

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 GOX

Atom Name (V3) Atom Name (V2)
C1 C1
N1 N1
C2 C2
N5 N5
O7 O7
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
C6 C6
O6 O6
HC2 HC2
HN5 HN5
HO7 HO7
HO2 HO2
HC3 HC3
HO3 HO3
HC4 HC4
HO4 HO4
HC5 HC5
HC61 1HC6
HC62 2HC6
HO6 HO6