Atom Nomenclature for KLN

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 KLN

Atom Name (V3) Atom Name (V2)
N1 N1
C1 C1
N2 N2
C2 C2
C3 C3
C4 C4
C5 C5
O1 O1
C6 C6
C7 C7
O2 O2
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
CL1 CL1
C14 C14
O3 O3
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
N3 N3
C21 C21
C22 C22
N4 N4
C23 C23
C24 C24
C25 C25
O4 O4
C26 C26
CL2 CL2
H1 H1
H3 H3
H4C1 1H4C
H4C2 2H4C
H2 H2
H6 H6
H7C1 1H7C
H7C2 2H7C
H141 1H14
H142 2H14
H13 H13
H10 H10
H12 H12
H20 H20
H16 H16
H19 H19
H17 H17
H211 1H21
H212 2H21
H241 1H24
H242 2H24
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H261 1H26
H262 2H26
H263 3H26