Atom Nomenclature for UGA

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 UGA

Atom Name (V3) Atom Name (V2)
C1' C1'
C2' C2'
O2' O2'
C3' C3'
O3' O3'
C4' C4'
O4' O4'
C5' C5'
O5' O5'
C6' C6'
O'P O6'1
O'Q O6'2
PB PB
O1B O1B
O2B O2B
O3B O3B
O3A O3A
PA PA
O1A O1A
O2A O2A
O5D O5*
C5D C5*
C4D C4*
O4D O4*
C3D C3*
O3D O3*
C2D C2*
O2D O2*
C1D C1*
N1 N1
C6 C6
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
H1'1 1H1'
H2'1 1H2'
HO'2 2HO'
H3'1 1H3'
HO'3 3HO'
H4'1 1H4'
HO'4 4HO'
H5'1 1H5'
HO'6 6HO'
HOB2 2HOB
HOA2 2HOA
H5A1 1H5*
H5'2 2H5*
H4A1 1H4*
H3A1 1H3*
HOA3 3HO*
H2A1 1H2*
HOC2 2HO*
H1A1 1H1*
H61 1H6
HN3 HN3
H51 1H5