Atom Nomenclature for K5P

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 K5P

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C7 C4
C8 C5
C9 C6
C10 C7
C11 C8
C12 C9
C13 C10
C14 C11
C15 C12
C16 C13
C19 C14
C20 C15
C21 C16
C22 C17
C24 C18
O3 O1
C26 C19
O2 O2
C18 C20
O O3
C17 C21
C23 C22
C25 C23
O1 O4
N N1
C C24
C5 C25
C4 C26
C6 C27
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27