Atom Nomenclature for 3AR

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 3AR

Atom Name (V3) Atom Name (V2)
N N
CA CA
C C
O O
CB CB
CG CG
CD CD
NE NE
CZ CZ
NH1 NH1
NH2 NH2
C1 C1
C2 C2
C3 C3
OXT OXT
H H
H2 HN2
HA HA
HB2 1HB
HB3 2HB
HG2 1HG
HG3 2HG
HD2 1HD
HD3 2HD
HE HE
HH1 1HH1
HH21 1HH2
HH22 2HH2
H11 1H1
H12 2H1
H21 1H2
H22 2H2
H31 1H3
H32 2H3
H33 3H3
HXT HXT