Atom Nomenclature for T8D

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 T8D

Atom Name (V3) Atom Name (V2)
N1 N1
C4 C1
C5 C2
C6 C3
C7 C4
C8 C5
N N2
C C6
O O1
C1 C7
C2 C8
C3 C9
C9 C10
O1 O2
O2 O3
S S1
S1 S2
CL CL1
H8 H1
H7 H2
H10 H3
H9 H4
H11 H5
H12 H6
H H7
H1 H8
H2 H9
H4 H10
H3 H11
H6 H12
H5 H13