Atom Nomenclature for BR4

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 BR4

Atom Name (V3) Atom Name (V2)
C9 C9
C8 C8
C7 C7
C6 C6
C1 C1
C5 C5
C2 C2
C4 C4
C3 C3
C13 C13
O1 O1
C12 C12
C11 C11
C10 C10
N1 N1
C23 C23
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C22 C22
C19 C19
C21 C21
C20 C20
C24 C24
C25 C25
O2 O2
OT3 OT3
H91 1H9
H92 2H9
H81 1H8
H82 2H8
H71 1H7
H72 2H7
H11 1H1
H51 1H5
H21 1H2
H41 1H4
H31 1H3
H121 1H12
H122 2H12
H111 1H11
H112 2H11
H101 1H10
H102 2H10
HN11 1HN1
H231 1H23
H232 2H23
H141 1H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H181 1H18
H221 1H22
H191 1H19
H211 1H21
H201 1H20
H241 1H24
H242 2H24
HO31 1HO3