Atom Nomenclature for ENP

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 ENP

Atom Name (V3) Atom Name (V2)
P1 P1
O1 O1
O2 O2
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
O2' O2*
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
N6 N6
N1 N1
C2 C2
N3 N3
C4 C4
O3 O3
P2 P2
O4 O4
O5 O5
O9' O9*
C0' C0*
C9' C9*
O8' O8*
C8' C8*
O7' O7*
C7' C7*
O6' O6*
C6' C6*
P3 P3
O7 O7
O8 O8
O9 O9
C1 C1
C9 C9
O6 O6
HO1 HO1
H5' 1H5*
H5'' 2H5*
H4' H4*
H3' H3*
HO3 HO3
H2' H2*
H1' H1*
H8 H8
H2 H2
HO4 HO4
H0'1 1H0*
H0'2 2H0*
H9' H9*
H8' H8*
HO'7 7HO*
H7' H7*
HO'6 6HO*
H6' H6*
HO7 HO7
HO8 HO8
H1 H1
H9 H9
HO6 HO6