Atom Nomenclature for D92

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 D92

Atom Name (V3) Atom Name (V2)
CL1 CL1
C16 C16
C17 C17
C18 C18
C12 C12
N11 N11
C15 C15
C13 C13
C14 C14
C10 C10
C9 C9
O19 O19
N7 N7
C1 C1
C6 C6
C5 C5
C4 C4
C3 C3
C2 C2
N8 N8
C20 C20
O31 O31
C21 C21
S25 S25
C24 C24
C26 C26
N27 N27
C30 C30
C28 C28
C29 C29
C23 C23
N22 N22
H17 H17
H18 H18
HN11 HN11
H15 H15
H14 H14
HN7 HN7
H1 H1
H61 1H6
H62 2H6
H51 1H5
H52 2H5
H41 1H4
H42 2H4
H31 1H3
H32 2H3
H2 H2
HN8 HN8
H261 1H26
H262 2H26
H301 1H30
H302 2H30
H303 3H30
H281 1H28
H282 2H28
H291 1H29
H292 2H29