Atom Nomenclature for MNU

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 MNU

Atom Name (V3) Atom Name (V2)
P P
OP2 O2P
OP1 O1P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C1' C1*
N1 N1
C6 C6
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C7 C7
N8 N8
C9 C9
C2' C2*
O2' O2*
C3' C3*
O3' O3*
OP3 O3P
HOP2 2HOP
H5' 1H5*
H5'' 2H5*
H4' H4*
H1' H1*
H6 H6
HN3 HN3
H71 1H7
H72 2H7
HN8 HN8
H91 1H9
H92 2H9
H93 3H9
H2' H2*
HO2' 2HO*
H3' H3*
HO3' H3T
HOP3 3HOP