Atom Nomenclature for N8M

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 N8M

Atom Name (V3) Atom Name (V2)
CG CG
N2 N2
CE CE
C5' C5*
C4' C4*
O4' O4*
C1' C1*
N9 N9
C4 C4
N3 N3
C2 C2
N1 N1
C6 C6
N6 N6
C5 C5
N7 N7
C8 C8
C2' C2*
O2' O2*
C3' C3*
O3' O3*
C9 C9
HG HG
HGA HGA
HGB HGB
HE HE
HEA HEA
HEB HEB
H5' H5*
H5'A H5*A
H4' H4*
H1' H1*
H2 H2
HN6 HN6
HN6A HN6A
H2' H2*
HO2' HO2*
H3' H3*
HO3' HO3*
H9 H9
H9A H9A
H9B H9B