Atom Nomenclature for KEF

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 KEF

Atom Name (V3) Atom Name (V2)
C14 C14
O15 O15
C16 C16
C17 C17
C19 C19
C18 C18
O17 O17
N16 N16
C4' C4'
C3' C3'
C11 C11
C13 C13
C2 C2
C3 C3
C4 C4
C6 C6
C7 C7
C8 C8
N10 N10
N5 N5
O4A O4A
O4B O4B
O12 O12
O9 O9
S1 S1
O3' O3'
C31 C31
O31 O31
N31 N31
H16 H16
H17 H17
H19 H19
H183 3H18
H182 2H18
H181 1H18
H3'2 2H3'
H3'1 1H3'
H2 H2
H4 H4
H6 H6
H7 H7
H10 H10
H4O H4O
HN31 1HN3
HN32 2HN3