Atom Nomenclature for 9K8

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 9K8

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
O4 O1
O5 O2
C7 C4
C8 C5
C9 C6
C10 C7
C11 C8
C12 C9
C13 C10
C14 C11
C15 C12
C16 C13
O2 O3
C5 C14
C4 C15
C6 C16
S S1
O1 O4
O O5
C C17
O3 O6
O6 O7
N N1
N2 N2
C17 C18
N3 N3
C18 C19
N4 N4
N1 N5
F F1
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
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21