Atom Nomenclature for T6M

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 T6M

Atom Name (V3) Atom Name (V2)
N1 N1
C4 C1
C5 C2
C6 C3
C7 C4
C8 C5
C10 C6
N N2
C C7
O O1
C1 C8
C11 C9
C2 C10
C3 C11
C9 C12
O1 O2
O2 O3
S S1
CL1 CL1
H7 H1
H6 H2
H9 H3
H8 H4
H10 H5
H11 H6
H12 H7
H H8
H14 H9
H1 H10
H13 H11
H3 H12
H2 H13
H5 H14
H4 H15