Atom Nomenclature for LBV

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 LBV

Atom Name (V3) Atom Name (V2)
C1A C1A
C1B C1B
O1B O1B
C1C C1C
O1C O1C
C1D C1D
C2A C2A
C2B C2B
O2B O2B
C2C C2C
O2C O2C
C2D C2D
C3A C3A
C3B C3B
C3C C3C
C3D C3D
C4A C4A
C4B C4B
C4C C4C
C4D C4D
CAA CAA
CAB CAB
CAC CAC
CAD CAD
CBA CBA
CBB CBB
CBC CBC
CBD CBD
CGB CGB
CGC CGC
CHB CHB
CHC CHC
CHD CHD
CMA CMA
CMB CMB
CMC CMC
CMD CMD
N_A N_A
O_A O_A
N_B N_B
N_C N_C
N_D N_D
O_D O_D
HO1C HO1C
H2A H2A
HO2B HO2B
HAA1 HAA1
HAB1 HAB1
HAB2 HAB2
HAC1 HAC1
HAC2 HAC2
HAD1 HAD1
HBA1 HBA1
HBA2 HBA2
HBA3 HBA3
HBB1 HBB1
HBB2 HBB2
HBC1 HBC1
HBC2 HBC2
HBD1 HBD1
HBD2 HBD2
HHB1 HHB1
HHC1 HHC1
HHD1 HHD1
HMA1 HMA1
HMA2 HMA2
HMA3 HMA3
HMB1 HMB1
HMB2 HMB2
HMB3 HMB3
HMC1 HMC1
HMC2 HMC2
HMC3 HMC3
HMD1 HMD1
HMD2 HMD2
HMD3 HMD3
HAD HAD
HAE HAE
HAF HAF
HAG HAG