Atom Nomenclature for GTG

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 GTG

Atom Name (V3) Atom Name (V2)
PA PA
O1A O1A
O2A O2A
O3A O3A
PB PB
O1B O1B
O2B O2B
O3B O3B
N9A N9A
C8A C8A
N7A N7A
C7X C7MA
C5A C5A
C6A C6A
O6A O6A
N1A N1A
C2A C2A
N2A N2A
N3A N3A
C4A C4A
O5D O5*A
C5D C5*A
C4D C4*A
O4D O4*A
C3D C3*A
O3D O3*A
C2D C2*A
O2D O2*A
C1D C1*A
PG PG
O1G O1G
O2G O2G
O5E O5*B
C5E C5*B
C4E C4*B
O4E O4*B
C3E C3*B
O3E O3*B
C2E C2*B
O2E O2*B
C1E C1*B
N9B N9B
C8B C8B
N7B N7B
C5B C5B
C6B C6B
O6B O6B
N1B N1B
C2B C2B
N2B N2B
N3B N3B
C4B C4B
HOA2 2HOA
HOB2 2HOB
H8 H8
HC71 1HC7
HC72 2HC7
HC73 3HC7
HN1 HN1
HN21 1HN2
HN22 2HN2
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HO3' *HO3
H2' H2*
HO2' *HO2
H1' H1*
HOG2 2HOG
H5B1 1H5B
H5B2 2H5B
H4B H4B
H3B H3B
H3BO OH3B
H2B H2B
H2BO OH2B
H1B H1B
H8B H8B
H1BN NH1B
H2B1 1H2B
H2B2 2H2B