Atom Nomenclature for 87Y

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 87Y

Atom Name (V3) Atom Name (V2)
N2 N2
C3 C3
O8 O8
C7 C7
N10 N10
C12 C12
C15 C15
O16 O16
C11 C11
C14 C14
C13 C13
N9 N9
C6 C6
N4 N4
C1 C1
N5 N5
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
H2 H2
H152 2H15
H151 1H15
H16 H16
H142 2H14
H141 1H14
H133 3H13
H132 2H13
H131 1H13
H9 H9
H52 2H5
H51 1H5
H172 2H17
H171 1H17
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23