Atom Nomenclature for G1C

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 G1C

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
N2 N2
N3 N3
C4 C4
C5 C5
C6 C6
O6 O6
N7 N7
C8 C8
N9 N9
PA PA
PB PB
PG PG
C1' C1'
O1A O1A
O1B O1B
O1G O1G
C2' C2'
O2A O2A
O2B O2B
O2G O2G
C3' C3'
O3' O3'
O3A O3A
C3B C3B
CL3B CL3B
O3G O3G
C4' C4'
O4' O4'
C5' C5'
O5' O5'
HN1 HN1
HN2 HN2
HN2A HN2A
H8 H8
H1' H1'
H2' H2'
H2'A H2'A
H3' H3'
HO3' HO3'
H3B H3B
H4' H4'
H5' H5'
H5'A H5'A
H14 H14
H15 H15
H16 H16
H17 H17