Atom Nomenclature for DXC

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 DXC

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
O1 O1
O2 O2
C20 C20
C21 C21
C22 C22
C23 C23
O3 O3
O4 O4
C24 C24
H1 H1
H22 2H2
H21 1H2
H3 H3
H52 2H5
H51 1H5
H62 2H6
H61 1H6
H72 2H7
H71 1H7
H82 2H8
H81 1H8
H9 H9
H10 H10
H11 H11
H13 H13
H142 2H14
H141 1H14
H152 2H15
H151 1H15
H162 2H16
H161 1H16
H17 H17
H183 3H18
H182 2H18
H181 1H18
H19 H19
H1O1 1H1O
H2 H2
H203 3H20
H202 2H20
H201 1H20
H212 2H21
H211 1H21
H222 2H22
H221 1H22
HO4 HO4
H243 3H24
H242 2H24
H241 1H24