Atom Nomenclature for ZIT

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 ZIT

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
N10 N10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
O1 O1
O6 O6
O12 O12
O13 O13
O14 O14
C1A C1A
C2A C2A
C3A C3A
C4A C4A
C5A C5A
C6A C6A
C7A C7A
C8A C8A
O1A O1A
O2A O2A
N3A N3A
O5A O5A
C1B C1B
C2B C2B
C3B C3B
C4B C4B
C5B C5B
C6B C6B
C7B C7B
C8B C8B
O1B O1B
O3B O3B
O4B O4B
O5B O5B
H2 H2
H3 H3
H4 H4
H5 H5
H71 1H7
H72 2H7
H8 H8
H91 1H9
H92 2H9
H11 H11
H12 H12
H14 H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H163 3H16
H171 1H17
H172 2H17
H173 3H17
H181 1H18
H182 2H18
H183 3H18
H191 1H19
H192 2H19
H193 3H19
H201 1H20
H202 2H20
H203 3H20
H211 1H21
H212 2H21
H213 3H21
H221 1H22
H222 2H22
H223 3H22
H231 1H23
H232 2H23
H233 3H23
HO6 HO6
HO12 HO12
HO13 HO13
H1A1 1H1A
H2A1 1H2A
H3A1 1H3A
H4A1 1H4A
H4A2 2H4A
H5A1 1H5A
H6A1 1C6A
H6A2 2C6A
H6A3 3C6A
H7A1 1H7A
H7A2 2H7A
H7A3 3H7A
H8A1 1H8A
H8A2 2H8A
H8A3 3H8A
HO2A HO2A
H1B1 1H1B
H2B1 1H2B
H2B2 2H2B
H4B1 1H4B
H5B1 1H5B
H6B1 1C6B
H6B2 2C6B
H6B3 3C6B
H7B1 1H7B
H7B2 2H7B
H7B3 3H7B
H8B1 1H8B
H8B2 2H8B
H8B3 3H8B
HO4B HO4B