Atom Nomenclature for HRG

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 HRG

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
CG CG
CG' CG'
CD CD
NE NE
CZ CZ
NH1 NH1
NH2 NH2
C C
O O
OXT OXT
HN1A 1HN
HN2 2HN
HA HA
HB1 1HB
HB2 2HB
HG1 1HG
HG2 2HG
HG'1 1HG'
HG'2 2HG'
HD1 1HD
HD2 2HD
HNE HNE
HN1 HN1
HN21 1HN2
HN22 2HN2
HXT HXT