Atom Nomenclature for LY0

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 LY0

Atom Name (V3) Atom Name (V2)
P P
C1 C1
N1 N1
C2 C2
C4 C4
C5 C5
C6 C6
C7 C7
O31 O31
O32 O32
O61 O61
O62 O62
H1 H1
H1A H1A
H1B H1B
HN1 HN1
HN1A HN1A
H2 H2
H4 H4
H4A H4A
H5 H5
H7 H7
H7A H7A
H7B H7B
HO32 HO32
HO61 HO61