Atom Nomenclature for LME

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 LME

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
C1 C1
CG CG
CD CD
OE1 OE1
OE2 OE2
C C
O O
H2 H2
H H
HA HA
HB HB
H11 H11
H12 H12
H13 H13
HG2 HG2
HG3 HG3
HE2 HE2
OXT OXT
HXT HXT