Atom Nomenclature for SOR

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 SOR

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
O1 O1
O2 O2
O3 O3
O4 O4
O5 O5
O6 O6
H11 1H1
H12 2H1
H2 H2
H3 H3
H4 H4
H5 H5
H61 1H6
H62 2H6
HO1 HO1
HO2 HO2
HO3 HO3
HO4 HO4
HO5 HO5
HO6 HO6