Atom Nomenclature for GNP

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 GNP

Atom Name (V3) Atom Name (V2)
PG PG
O1G O1G
O2G O2G
O3G O3G
N3B N3B
PB PB
O1B O1B
O2B O2B
O3A O3A
PA PA
O1A O1A
O2A O2A
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
HOG2 2HOG
HOG3 3HOG
HNB3 3HNB
HOB2 2HOB
HOA2 2HOA
H5'2 2H5*
H5'1 1H5*
H4' H4*
H3' H3*
HO3' *HO3
H2' H2*
HO2' *HO2
H1' H1*
H8 H8
HN1 HN1
HN21 1HN2
HN22 2HN2