Atom Nomenclature for ORG

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 ORG

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
N3 N3
C4 C4
N5 N5
C6 C6
N7 N7
N8 N8
C9 C9
C10 C10
C11 C11
N12 N12
C13 C13
C14 C14
N15 N15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
HN7 HN7
H10 H10
H10A H10A
H11 H11
H11A H11A
HN12 HN12
H13 H13
H13A H13A
H14 H14
H14A H14A
H16 H16
H17 H17
H17A H17A
H18 H18
H18A H18A
H19 H19
H19A H19A
H20 H20
H20A H20A
H21 H21
H21A H21A