Atom Nomenclature for 4PD

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 4PD

Atom Name (V3) Atom Name (V2)
P P
OP1 O1P
OP2 O2P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
C1' C1*
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
C5 C5
C6 C6
C14 C14
C15 C15
C16 C16
N17 N17
OP3 O3P
HOP2 2HOP
H5' 1H5*
H5'' 2H5*
H4' H4*
H3' H3*
HO3' H3T
H2' 1H2*
H2'' 2H2*
H1' H1*
H19 H19
H6 H6
H14 H14
H161 1H16
H162 2H16
H163 3H16
HOP3 3HOP