Atom Nomenclature for DGX

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 DGX

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
O3 O3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
O12 O12
C13 C13
C14 C14
O14 O14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C1X C1X
C1Y C1Y
C1Z C1Z
C20 C20
C21 C21
O21 O21
C22 C22
C23 C23
O23 O23
C2X C2X
C2Y C2Y
C2Z C2Z
C3X C3X
O3X O3X
C3Y C3Y
O3Y O3Y
C3Z C3Z
O3Z O3Z
C4X C4X
O4X O4X
C4Y C4Y
O4Y O4Y
C4Z C4Z
O4Z O4Z
C5X C5X
O5X O5X
C5Y C5Y
O5Y O5Y
C5Z C5Z
O5Z O5Z
C6X C6X
C6Y C6Y
C6Z C6Z
H1 H1
H1A H1A
H2 H2
H2A H2A
H3 H3
H4 H4
H4A H4A
H5 H5
H6 H6
H6A H6A
H7 H7
H7A H7A
H8 H8
H9 H9
H11 H11
H11A H11A
H12 H12
HO12 HO12
HO14 HO14
H15 H15
H15A H15A
H16 H16
H16A H16A
H17 H17
H18 H18
H18A H18A
H18B H18B
H19 H19
H19A H19A
H19B H19B
H1X H1X
H1Y H1Y
H1Z H1Z
H21 H21
H21A H21A
H22 H22
H2X H2X
H2XA H2XA
H2Y H2Y
H2YA H2YA
H2Z H2Z
H2ZA H2ZA
H3X H3X
HO3X HO3X
H3Y H3Y
HO3Y HO3Y
H3Z H3Z
HO3Z HO3Z
H4X H4X
H4Y H4Y
H4Z H4Z
HO4Z HO4Z
H5X H5X
H5Y H5Y
H5Z H5Z
H6X H6X
H6XA H6XA
H6XB H6XB
H6Y H6Y
H6YA H6YA
H6YB H6YB
H6Z H6Z
H6ZA H6ZA
H6ZB H6ZB