Atom Nomenclature for YYG

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 YYG

Atom Name (V3) Atom Name (V2)
P P
OP1 O1P
OP2 O2P
OP3 O3P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
O2' O2*
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
O6 O6
N1 N1
C2 C2
N2 N2
N3 N3
C3 C3
C4 C4
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
O17 O17
O18 O18
C19 C19
N20 N20
C21 C21
O22 O22
O23 O23
C24 C24
HOP2 2HOP
HOP3 3HOP
H5' 1H5*
H5'' 2H5*
H4' H4*
H3' H3*
HO3' H3T
H2' H2*
HO2' 2HO*
H1' H1*
H8 H8
H31 1H3
H32 2H3
H33 3H3
H101 1H10
H102 2H10
H103 3H10
H131 1H13
H132 2H13
H141 1H14
H142 2H14
H15 H15
H191 1H19
H192 2H19
H193 3H19
HN20 HN20
H241 1H24
H242 2H24
H243 3H24