Atom Nomenclature for PCN

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 PCN

Atom Name (V3) Atom Name (V2)
O1 O1
C1 C1
C2 C2
C3 C3
S4 S4
C5 C5
C51 C51
C52 C52
C6 C6
C61 C61
O62 O62
O63 O63
N7 N7
N8 N8
C9 C9
O91 O91
C10 C10
N11 N11
O12 O12
C13 C13
C14 C14
C15 C15
S16 S16
C17 C17
N18 N18
N19 N19
HC1 HC1
HC2 HC2
HC3 HC3
H511 1H51
H512 2H51
H513 3H51
H521 1H52
H522 2H52
H523 3H52
HC6 HC6
H63O OH63
HN7 HN7
HN8 HN8
H131 1H13
H132 2H13
H133 3H13
H15 H15
H191 1H19
H192 2H19