Atom Nomenclature for BOR

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 BOR

Atom Name (V3) Atom Name (V2)
O1 O1
B B
O2 O2
CA CA
N N
CB CB
CG CG
CD CD
NE NE
CZ CZ
NH1 NH1
NH2 NH2
HO1 HO1
HO2 HO2
HA HA
H HN1
H2 HN2
HB1 HB1
HB2 HB2
HG1 HG1
HG2 HG2
HD1 HD1
HD2 HD2
HNE HNE
HH1 HH1
HH21 HH21
HH22 HH22