Atom Nomenclature for CQA

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 CQA

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
N1 N1
CL CL
N2 N2
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
O O
C16 C16
N3 N3
C17 C17
C18 C18
C19 C19
C20 C20
H2 H2
H3 H3
H6 H6
H8 H8
H9 H9
HN2 HN2
H11 H11
H12 H12
H15 H15
HO HO
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H181 1H18
H182 2H18
H183 3H18
H191 1H19
H192 2H19
H201 1H20
H202 2H20
H203 3H20