Atom Nomenclature for ALN

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 ALN

Atom Name (V3) Atom Name (V2)
N N
CA CA
C C
O O
CB CB
CG1 CG1
CD1 CD1
CE1 CE1
CD2 CD2
CE2 CE2
CZ1 CZ1
CG2 CG2
CD3 CD3
CE3 CE3
CZ2 CZ2
OXT OXT
H 1HN
H2 2HN
HA HA
HB2 1HB
HB3 2HB
HD1 HD1
HE1 HE1
HZ1 HZ1
HG2 HG2
HD3 HD3
HE3 HE3
HZ2 HZ2
HXT HXT