Atom Nomenclature for PNX

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 PNX

Atom Name (V3) Atom Name (V2)
CAA CAA
CAM CAM
OAD OAD
CAJ CAJ
CAH CAH
CAI CAI
CAK CAK
N1 N1
C6 C6
O6 O6
C5 C5
N7 N7
CAB CAB
C8 C8
N9 N9
C4 C4
N3 N3
CAC CAC
C2 C2
O2 O2
HAA1 1HAA
HAA2 2HAA
HAA3 3HAA
HAJ1 1HAJ
HAJ2 2HAJ
HAH1 1HAH
HAH2 2HAH
HAI1 1HAI
HAI2 2HAI
HAK1 1HAK
HAK2 2HAK
HAB1 1HAB
HAB2 2HAB
HAB3 3HAB
H8 H8
HAC1 1HAC
HAC2 2HAC
HAC3 3HAC