Atom Nomenclature for TES

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 TES

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
O3 O3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
O17 O17
C18 C18
C19 C19
H11 1H1
H12 2H1
H21 1H2
H22 2H2
H4 H4
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H8 H8
H9 H9
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H14 H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H17 H17
HO7 HO7
H181 1H18
H182 2H18
H183 3H18
H191 1H19
H192 2H19
H193 3H19