Atom Nomenclature for D11

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 D11

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
CG2 CG2
OG1 OG1
P P
O1P O1P
O2P O2P
O3P O3P
C C
O O
OXT OXT
H HN1
H2 HN2
HA HA
HB HB
HG21 HG21
HG22 HG22
HG23 HG23
HO2P HO2P
HO3P HO3P
HXT HOXT