Atom Nomenclature for BN4

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 BN4

Atom Name (V3) Atom Name (V2)
C4 C4
C5 C5
C6 C6
C1 C1
CL1 CL1
C2 C2
C3 C3
N1 N1
C7 C7
O1 O1
N2 N2
C9 C9
C10 C10
C11 C11
C12 C12
O3 O3
C15 C15
C16 C16
C17 C17
C13 C13
C14 C14
C8 C8
O2 O2
CL2 CL2
C19 C19
C18 C18
O4 O4
O5 O5
C20 C20
H4 H4
H5 H5
H2 H2
HN1 HN1
HN2 HN2
H10 H10
H11 H11
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H191 1H19
H192 2H19
H193 3H19
HO4 HO4
H201 1H20
H202 2H20
H203 3H20