Atom Nomenclature for MSE

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 MSE

Atom Name (V3) Atom Name (V2)
N N
CA CA
C C
O O
OXT OXT
CB CB
CG CG
SE SE
CE CE
H 1HN
HN2 2HN
HA HA
HXT HXT
HB2 1HB
HB3 2HB
HG2 1HG
HG3 2HG
HE1 1HE
HE2 2HE
HE3 3HE