Atom Nomenclature for KWT

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 KWT

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C9 C9
C23 C23
C2 C2
O2 O2
C3 C3
C4 C4
C19 C19
C5 C5
C6 C6
O5 O5
O3 O3
C7 C7
O6 O6
C11 C11
C21 C21
C8 C8
C15 C15
C10 C10
C12 C12
C13 C13
C14 C14
C18 C18
C16 C16
C17 C17
O4 O4
O7 O7
C22 C22
O8 O8
C24 C24
HC1 HC1
H231 1H23
H232 2H23
H19 H19
H11 H11
H15 H15
H101 1H10
H102 2H10
H103 3H10
H121 1H12
H122 2H12
H141 1H14
H142 2H14
H143 3H14
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H221 1H22
H222 2H22
H223 3H22
H241 1H24
H242 2H24
H243 3H24