Atom Nomenclature for DK1

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 DK1

Atom Name (V3) Atom Name (V2)
O1 O1
C2 C2
O2 O2
C1 C1
N1 N1
C10 C10
C9 C9
C8 C8
CL2 CL2
C7 C7
C6 C6
CL1 CL1
C5 C5
C4 C4
O3 O3
C3 C3
HO1 HO1
H9 H9
H7 H7
HO3 HO3
H3 H3