Atom Nomenclature for THS

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 THS

Atom Name (V3) Atom Name (V2)
P P
O1P O1P
S2P S2P
S3P S3P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
C1' C1*
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C5M C5M
C6 C6
HSP2 2HSP
HSP3 3HSP
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HO3' *HO3
H2'1 1H2*
H2'2 2H2*
H1' H1*
HN3 HN3
HM51 1HM5
HM52 2HM5
HM53 3HM5
H6 H6