Atom Nomenclature for TRH

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 TRH

Atom Name (V3) Atom Name (V2)
O4P O4P
P2 P2
O3P O3P
O1 O1
C1 C1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
O5 O5
C6 C6
OPP OPP
P P
O1P O1P
O2P O2P
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
C1' C1'
N11 N11
C21 C21
O21 O21
N31 N31
C41 C41
O41 O41
C51 C51
C5A C5A
C61 C61
H4PO OH4P
HC1 HC1
HC2 HC2
HO2 HO2
HC3 HC3
HO3 HO3
HC4 HC4
HO4 HO4
HC5 HC5
HC61 1HC6
HC62 2HC6
HC63 3HC6
H1PO OH1P
H5'1 1H5'
H5'2 2H5'
H4'C CH4'
H3'C CH3'
H3'O OH3'
H2'1 1H2'
H2'2 2H2'
H1'C CH1'
H31N NH31
HCA1 1HCA
HCA2 2HCA
HCA3 3HCA
H61C CH61