Atom Nomenclature for XBJ

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 XBJ

Atom Name (V3) Atom Name (V2)
C01 C01
C02 C02
C03 C03
C04 C04
C05 C05
N06 N06
C07 C07
N08 N08
C09 C09
C10 C10
N11 N11
C12 C12
C13 C13
C14 C14
N15 N15
C16 C16
C17 C17
C18 C18
C19 C19
O20 O20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
F27 F27
O28 O28
O29 O29
C30 C30
O31 O31
C32 C32
H01 H01
H04 H04
H11 H11
H12 H12
H13 H13
H161 H161
H162 H162
H141 H141
H142 H142
H15 H15
H181 H181
H182 H182
H183 H183
H191 H191
H192 H192
H193 H193
H20 H20
H26 H26
H23 H23
H28 H28
H24 H24
H301 H301
H302 H302
H303 H303
H321 H321
H322 H322
H323 H323