Atom Nomenclature for BZG

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 BZG

Atom Name (V3) Atom Name (V2)
P P
O1P O1P
O2P O2P
O5' O5'
CZ1 CZ1
CT1 CT1
CI CI
CT2 CT2
CZ2 CZ2
CE CE
CW CW
OL OL
CK CK
NJ NJ
CH CH
NI NI
NG NG
CF CF
CM CM
NN NN
CO CO
NE NE
CT' CT'
OS' OS'
CP' CP'
C5' C5'
C4' C4'
C3' C3'
O3' O3'
OXT OXT
H1P H1P
HOT HOT
H5'1 H5'1
H5'2 H5'2
HZ1 HZ1
HT1 HT1
HI HI
HT2 HT2
HZ2 HZ2
HWC1 HWC1
HWC2 HWC2
HIN1 HIN1
HIN2 HIN2
HO HO
HT' HT'
HP'1 HP'1
HP'2 HP'2
H4' H4'
H3' H3'
HA HA