Atom Nomenclature for 60V

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 60V

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C1
C3 C2
C6 C3
C8 C4
C9 C5
C10 C6
C11 C7
C12 C8
C13 C9
C16 C10
C17 C11
F F1
C15 C12
C14 C13
N5 N2
O1 O1
N6 N3
N4 N4
O O2
N3 N5
C7 C14
N2 N6
C5 C15
C C16
C1 C17
S S1
C4 C18
N N7
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H18 H18
H19 H19