Atom Nomenclature for 5SF

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 5SF

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
O1 O1
C18 C19
O O2
C23 C20
C17 C21
N1 N1
C4 C22
N N2
C C23
C5 C24
N2 N3
N5 N4
N4 N5
N3 N6
C6 C25
H3 H1
H4 H2
H5 H3
H6 H4
H9 H5
H8 H6
H13 H7
H14 H8
H15 H9
H16 H10
H17 H11
H19 H12
H20 H13
H18 H14
H22 H15
H23 H16
H28 H17
H27 H18
H29 H19
H21 H20
H24 H21
H25 H22
H26 H23
H11 H24
H10 H25
H7 H26
H H28
H2 H29
H1 H30
H12 H31