Atom Nomenclature for CTC

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 CTC

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
C2' C2'
O2' O2'
N2' N2'
C3 C3
O3 O3
C4 C4
N4 N4
C4' C4'
C4D C4"
C4A C4A
C5 C5
C5A C5A
C6 C6
O6 O6
C6' C6'
C6A C6A
C7 C7
CL7 CL7
C8 C8
C9 C9
C10 C10
O10 O10
C6B C6B
C11 C11
O11 O11
C5B C5B
C12 C12
O12 O12
C4B C4B
O4B O4B
HN21 1HN2
HN22 2HN2
HO3 HO3
H4 H4
H4'1 1H4'
H4'2 2H4'
H4'3 3H4'
H4A1 1H4"
H4A2 2H4"
H4A3 3H4"
H4A H4A
H51 1H5
H52 2H5
H5A H5A
HO6 HO6
H6'1 1H6'
H6'2 2H6'
H6'3 3H6'
H8 H8
H9 H9
HO1 HO1
HO2 HO2
HO4 HO4