Atom Nomenclature for HEN

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 HEN

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
C2A C2A
C3 C3
O3 O3
C4 C4
C4A C4A
C5 C5
C6 C6
C5A C5A
OP4 OP4
P P
OP1 OP1
OP2 OP2
OP3 OP3
N4A N4A
CAI CAI
CBC CBC
O2B O2B
O3B O3B
CBI CBI
CGI CGI
CEI CEI
PG PG
OG1 OG1
OG2 OG2
OG3 OG3
H2A1 1H2A
H2A2 2H2A
H2A3 3H2A
HO3 HO3
H4A1 1H4A
H4A2 2H4A
HC6 HC6
H5A1 1H5A
H5A2 2H5A
HP1O OHP1
HP3O OHP3
H2BO OH2B
HBIC CHBI
HGIC CHGI
HCE1 1HCE
HCEC CHCE
HG1O OHG1
HG2O OHG2