Atom Nomenclature for T3S

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 T3S

Atom Name (V3) Atom Name (V2)
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
N26 N26
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
C1' C1'
N1 N1
C6 C6
C5 C5
C5M C5M
C4 C4
O4 O4
N3 N3
C2 C2
O2 O2
H21 H21
H21A H21A
H22 H22
H22A H22A
H23 H23
H23A H23A
H24 H24
H24A H24A
H25 H25
H25A H25A
H5' H5'
H5'A H5'A
H4' H4'
H3' H3'
HO3' HO3'
H2' H2'
H2'A H2'A
H1' H1'
H6 H6
H5M H5M
H5MA H5MA
H5MB H5MB
HN3 HN3