Atom Nomenclature for TST

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 TST

Atom Name (V3) Atom Name (V2)
S1 S1
C1 C1
C2 C2
N1 N1
C3 C3
C4 C4
C5 C5
N2 N2
O1 O1
C6 C6
C7 C7
C8 C8
O2 O2
O3 O3
C9 C9
C10 C10
S2 S2
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
O4 O4
O5 O5
C18 C18
H11 1H1
H12A 2H1
H21 1H2
H22 2H2
H3 H3
H41 1H4
H42 2H4
HN2 HN2
H6 H6
H71 1H7
H72 2H7
HO2 HO2
H9 H9
H101 1H10
H102 2H10
H103 3H10
H12 H12
H13 H13
H15 H15
H16 H16
H171 1H17
H172 2H17
H173 3H17
H181 1H18
H182 2H18
H183 3H18