Atom Nomenclature for 7PG

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 7PG

Atom Name (V3) Atom Name (V2)
OXT OXT
C1 C1
C2 C2
O1 O1
C3 C3
C4 C4
O2 O2
C5 C5
C6 C6
O3 O3
C7 C7
C8 C8
O4 O4
C9 C9
C10 C10
O5 O5
C11 C11
C12 C12
O6 O6
C13 C13
C14 C14
O7 O7
C15 C15
C16 C16
O8 O8
C17 C17
HOXT HOXT
H11 1H1
H12 2H1
H21 1H2
H22 2H2
H31 1H3
H32 2H3
H41 1H4
H42 2H4
H51 1H5
H52 2H5
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H81 1H8
H82 2H8
H91 1H9
H92 2H9
H101 1H10
H102 2H10
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H173 3H17