Atom Nomenclature for RET

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 RET

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
O1 O1
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
H21 H21
H22 H22
H31 H31
H32 H32
H41 H41
H42 H42
H7 H7
H8 H8
H10 H10
H11 H11
H12 H12
H14 H14
H15 H15
H161 H161
H162 H162
H163 H163
H171 H171
H172 H172
H173 H173
H181 H181
H182 H182
H183 H183
H191 H191
H192 H192
H193 H193
H201 H201
H202 H202
H203 H203