Atom Nomenclature for CCZ

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 CCZ

Atom Name (V3) Atom Name (V2)
P P
C1 C1
N1 N1
C2 C2
N2 N2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C01 C01
C02 C02
C03 C03
C04 C04
C05 C05
C06 C06
OP1 OP1
OP2 OP2
OP3 OP3
HN1 HN1
HN2 HN2
HN2A HN2A
H3 H3
H4 H4
H6 H6
H7 H7
H8 H8
H8A H8A
H02 H02
H03 H03
H04 H04
H05 H05
H06 H06
HOP3 HOP3