Atom Nomenclature for BO2

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 BO2

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
C3 C3
N4 N4
C5 C5
C6 C6
C7 C7
O8 O8
N9 N9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
O19 O19
N20 N20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
B26 B26
O27 O27
O28 O28
H3 H3
H5 H5
H6 H6
HN9 HN9
H10 H10
H111 1H11
H112 2H11
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H20 H20
H21 H21
H221 1H22
H222 2H22
H23 H23
H241 1H24
H242 2H24
H243 3H24
H251 1H25
H252 2H25
H253 3H25
H27 H27
H28 H28