Atom Nomenclature for 03X

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 03X

Atom Name (V3) Atom Name (V2)
N1 N1
N3 N3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C10 C10
C13 C13
C15 C15
C17 C17
C20 C20
C21 C21
C22 C22
C24 C24
C26 C26
C28 C28
C11 C11
O3 O3
C2 C2
C3 C3
C1 C1
O2 O2
C12 C12
C9 C9
O1 O1
C14 C14
F1 F1
C16 C16
N2 N2
C18 C18
O4 O4
C19 C19
O5 O5
C23 C23
N4 N4
C25 C25
C27 C27
C29 C29
H4 H4
H7 H7
H8 H8
H17 H17
H22 H22
H22A H22A
H22B H22B
H26 H26
H28 H28
H11 H11
H11A H11A
H11B H11B
H3 H3
H12 H12
H12A H12A
H12B H12B
H14 H14
H16 H16
HN2 HN2
H23 H23
H23A H23A
H23B H23B
H25 H25
H27 H27
H29 H29