Atom Nomenclature for STT

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 STT

Atom Name (V3) Atom Name (V2)
OAD O1
SBN S1
OAB O2
OAC O3
CAX C1
CAV C2
NBM N1
CBI C3
OAA O4
CBJ C4
SAE S2
SBA S3
CBK C5
CAG C6
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
C5 C7
C1 C8
N2 N2
N1 N3
C4 C9
C2 C10
C3 C11
C6 C12
C7 C13
C8 C14
C9 C15
C10 C16
C11 C17
C12 C18
C13 C19
C14 C20
C15 C21
O1 O5
C17 C22
C18 C23
C19 C24
C20 C25
C21 C26
C22 C27
F1 F1
H8 H8
H6 H6
H7 H7
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20