Atom Nomenclature for 5GP

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 5GP

Atom Name (V3) Atom Name (V2)
P P
O1P O1P
O2P O2P
O3P O3P
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
O6 O6
N1 N1
C2 C2
N2 N2
N3 N3
C4 C4
HOP2 2HOP
HOP3 3HOP
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HO3' *HO3
H2' H2*
HO2' *HO2
H1' H1*
H8 H8
HN1 HN1
HN21 1HN2
HN22 2HN2