Atom Nomenclature for IX1

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 IX1

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
O12 O12
N13 N13
C14 C14
C15 C15
C16 C16
O1 O1
O2 O2
C8 C8
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
O11 O11
O13 O13
C39 C39
O14 O14
O3 O3
C40 C40
C41 C41
C9 C9
O4 O4
H1 H1
H3 H3
H5 H5
H6 H6
HO1 HO1
H8 H8
H33 H33
H34 H34
H35 H35
H391 1H39
H392 2H39
H393 3H39
H14 H14
H401 1H40
H402 2H40
H41 H41
H91 1H9
H92 2H9
HO4 HO4