Atom Nomenclature for 77Y

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 77Y

Atom Name (V3) Atom Name (V2)
C6 C1
C1 C2
C29 C3
C28 C4
C27 C5
C30 C6
C5 C7
C4 C8
C3 C9
C2 C10
C14 C11
C16 C12
O34 O1
C32 C13
C33 C14
C12 C15
N15 N1
C13 C16
N9 N2
C7 C17
O4 O2
N3 N3
O2 O3
N1 N4
C1' C18
C2' C19
C3' C20
O3' O4
O4' O5
C4' C21
C5' C22
O5' O6
P P1
OP1 O7
OP2 O8
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H25 H25
OP3 OP3
H27 H27