Atom Nomenclature for SA0

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 SA0

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
O5 O5
C6 C6
O6 O6
OAA OAA
CAF CAF
CAG CAG
CAH CAH
CAI CAI
CAJ CAJ
CAN CAN
CAO CAO
H1 H1
H2 H2
HO2 HO2
H3 H3
HO3 HO3
H4 H4
HO4 HO4
H5 H5
H61 H6
H62 H6A
HO6 HO6
HOAA HOAA
HAF HAF
HAG HAG
HAH HAH
HAI HAI
HAJ HAJ
HAJA HAJA