Atom Nomenclature for A24

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 A24

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
O5 O5
C6 C6
O6 O6
C1' C1'
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
N1' N1'
O1' O1'
O2' O2'
C7' C7'
O3' O3'
N2' N2'
O1B O1*
C2B C2*
C3B C3*
N4' N4*
C5B C5*
C6B C6*
C7B C7*
C8' C8*
H11 1H1
H21 1H2
HO21 1HO2
H31 1H3
HO31 1HO3
H41 1H4
HO41 1HO4
H51 1H5
H61 1H6
H62 2H6
HO1 1HO
H2'1 1H2'
H4'1 1H4'
H6'1 1H6'
HN21 1HN2
H2A1 1H2*
H2'2 2H2*
H3'1 1H3*
H3'2 2H3*
H5'1 1H5*
H5'2 2H5*
H6A1 1H6*
H6'2 2H6*
H7'1 1H7*
H7'2 2H7*
H8'1 1H8*
H8'2 2H8*