Atom Nomenclature for 18M

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 18M

Atom Name (V3) Atom Name (V2)
P P
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
C4 C4
P1 P1
O11 O11
O12 O12
O13 O13
CM2 CM2
OP1 OP1
OP2 OP2
OP3 OP3
H5' H5'
H5'A H5'A
H4' H4'
H3' H3'
H2' H2'
H1' H1'
H8 H8
HN2 HN2
HN2A HN2A
HN3 HN3
HO11 HO11
HO13 HO13
HM2 HM2
HM2A HM2A
HM2B HM2B
HOP1 HOP1
HOP3 HOP3