Atom Nomenclature for DHE

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 DHE

Atom Name (V3) Atom Name (V2)
FE FE
CHA CHA
CHB CHB
CHC CHC
CHD CHD
NA N A
C1A C1A
C2A C2A
C3A C3A
C4A C4A
CMA CMA
CAA CAA
CBA CBA
CGA CGA
O1A O1A
O2A O2A
NB N B
C1B C1B
C2B C2B
OMB OMB
C3B C3B
CGB CGB
CAB CAB
CBB CBB
O1B O1B
O2B O2B
C4B C4B
NC N C
C1C C1C
C2C C2C
OMC OMC
C3C C3C
CGC CGC
CAC CAC
CBC CBC
O1C O1C
O2C O2C
C4C C4C
ND N D
C1D C1D
C2D C2D
C3D C3D
C4D C4D
CMD CMD
CAD CAD
CBD CBD
CGD CGD
O1D O1D
O2D O2D
HHA HHA
HHB HHB
HHC HHC
HHD HHD
HMA1 HMA1
HMA2 HMA2
HMA3 HMA3
HAA1 HAA1
HAA2 HAA2
HBA1 HBA1
HBA2 HBA2
H2A H2A
HGB1 HGB1
HGB2 HGB2
HGB3 HGB3
HAB1 HAB1
HAB2 HAB2
H2B H2B
HGC1 HGC1
HGC2 HGC2
HGC3 HGC3
HAC1 HAC1
HAC2 HAC2
H2C H2C
HMD1 HMD1
HMD2 HMD2
HMD3 HMD3
HAD1 HAD1
HAD2 HAD2
HBD1 HBD1
HBD2 HBD2
H2D H2D