Atom Nomenclature for BG6

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 BG6

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
O1 O1
O5 O5
C3 C3
O2 O2
C4 C4
O3 O3
C5 C5
O4 O4
C6 C6
O6 O6
P P
O1P O1P
O2P O2P
O3P O3P
H1 HC1
H2 HC2
HO1 HO1
H3 HC3
HO2 HO2
H4 HC4
HO3 HO3
H5 HC5
HO4 HO4
H61 HC61
H62 HC62
H1O1 H1O1
H2O2 H2O2