Atom Nomenclature for SEE

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 SEE

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
OG OG
B B
O1B O1B
O2B O2B
O3B O3B
C C
O O
H H
H2 H2
HA HA
HB2 HB2
HB3 HB3
OXT OXT
H6 H6
H7 H7
H8 H8
HXT HXT