Atom Nomenclature for CO4

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 CO4

Atom Name (V3) Atom Name (V2)
N2' N2*
C2D C2*
N3' N3*
C4D C4*
N4' N4*
C4A C4A
C5D C5*
C6D C6*
C7' C7*
N8' N8*
C8A C8A
N1' N1*
C8' C8*
N9' N9*
C1' C1'
C6' C6'
C5' C5'
O5' O5'
C5B C5B
C4' C4'
O4' O4'
C4B C4B
C3' C3'
O3' O3'
C3B C3B
C2' C2'
C9' C9*
C51 C51
H2'1 1H2*
H2'2 2H2*
H4'1 1H4*
H4'2 2H4*
H7' H7*
H8'1 1H8*
H8'2 2H8*
H6' H6'
H5B1 1H5B
H5B2 2H5B
H5B3 3H5B
H4B1 1H4B
H4B2 2H4B
H4B3 3H4B
H3B1 1H3B
H3B2 2H3B
H3B3 3H3B
H2' H2'
H9'1 1H9*
H9'2 2H9*
H9'3 3H9*
H511 1H51
H512 2H51
H513 3H51