Atom Nomenclature for FKY

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 FKY

Atom Name (V3) Atom Name (V2)
C5 C1
C6 C2
C7 C3
C8 C4
C10 C5
C15 C6
C20 C7
C22 C8
C24 C9
C26 C10
C28 C11
C1 C12
N2 N1
C3 C13
N4 N2
C9 C14
N11 N3
C12 C15
O13 O1
C14 C16
C16 C17
N17 N4
C18 C18
C19 C19
O21 O2
C23 C20
C25 C21
C27 C22
O29 O3
C30 C23
F31 F1
F32 F2
F33 F3
F34 F4
C35 C24
N36 N5
O37 O4
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