Atom Nomenclature for JZU

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 JZU

Atom Name (V3) Atom Name (V2)
S S
N1 N1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
N6 N6
N7 N7
C8 C8
N9 N9
C1' C1*
N18 N18
C2' C2*
O2' O2*
O2S O2S
C3' C3*
O3' O3*
O3S O3S
C4' C4*
O4' O4*
C5' C5*
N5' N5*
H2 H2
HN6 HN6
HN6A HN6A
H8 H8
H1' H1*
HN18 HN18
HN1A HN1A
H2' H2*
HO2' HO2*
H3' H3*
HO3' HO3*
H4' H4*
H5' H5*
H5'A H5*A
HN5' HN5*