Atom Nomenclature for TFR

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 TFR

Atom Name (V3) Atom Name (V2)
N N
O O
C1 C1
O1 O1
CA CA
CB CB
CC CC
CD CD
FE FE
FF FF
FG FG
CA1 CA1
CB1 CB1
OB1 OB1
CD1 CD1
CE1 CE1
CG1 CG1
OH1 OH1
CZ1 CZ1
NZ1 NZ1
HN HN
HA HA
HB HB
HBA HBA
HBB HBB
HC HC
HA1 HA1
HA1A HA1A
HB1 HB1
HB1A HB1A
HOB1 HOB1
HD1 HD1
HD1A HD1A
HE1 HE1
HG1 HG1
HG1A HG1A
HOH1 HOH1
HNZ1 HNZ1
HNZA HNZA