Atom Nomenclature for F42

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 F42

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C4A C4A
C5 C5
C5A C5A
C6 C6
C7 C7
C8 C8
O8M O8M
C9 C9
C9A C9A
N10 N10
C10 C10
C1' C1*
C2' C2*
O2' O2*
C3' C3*
O3' O3*
C4' C4*
O4' O4*
C5' C5*
O5' O5*
P P
O1P O1P
O2P O2P
O3P O3P
C1I C1I
C2I C2I
C3I C3I
O3I O3I
N1H N1H
C1H C1H
C2H C2H
O2U O2U
O2T O2T
C3H C3H
C4H C4H
C5H C5H
O5H O5H
N1G N1G
C1G C1G
C2G C2G
O2V O2V
O2W O2W
C3G C3G
C4G C4G
C5G C5G
O6G O6G
O7G O7G
HN3 HN3
H5 H5
H6 H6
HC7 HC7
HM81 1HM8
H9 H9
H1'1 1H1*
H1'2 2H1*
H2' H2*
HO2' *HO2
H3' H3*
HO3' *HO3
H4' H4*
HO4' *HO4
H5'1 1H5*
H5'2 2H5*
HOP2 2HOP
H1I1 1H1I
H2I1 1H2I
H2I2 2H2I
H2I3 3H2I
HNH1 1HNH
H1H1 1H1H
HXU HXU
H3H1 1H3H
H3H2 2H3H
H4H1 1H4H
H4H2 2H4H
HNG1 1HNG
H1G1 1H1G
HXV HXV
H3G1 1H3G
H3G2 2H3G
H4G1 1H4G
H4G2 2H4G
HXT HXT