Atom Nomenclature for AFG

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 AFG

Atom Name (V3) Atom Name (V2)
OP3 O3P
P P
OP1 O1P
OP2 O2P
O5' O5*
N9 N9
C4 C4
N3 N3
C2 C2
N2 N2
N1 N1
C6 C6
O6 O6
C5 C5
N7 N7
C8 C8
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
C40 C40
C41 C41
C42 C42
C43 C43
N29 N29
C2' C2*
C5' C5*
C4' C4*
O4' O4*
C1' C1*
C3' C3*
O3' O3*
HOP3 3HOP
HOP2 2HOP
HN21 1HN2
HN22 2HN2
HN1 HN1
H31 H31
H33 H33
H36 H36
H371 1H37
H372 2H37
H40 H40
H41 H41
H42 H42
H43 H43
H29 H29
H2' 1H2*
H2'' 2H2*
H5' 1H5*
H5'' 2H5*
H4' H4*
H1' H1*
H3' H3*
HO3' H3T