Atom Nomenclature for G36

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 G36

Atom Name (V3) Atom Name (V2)
P P
O1P O1P
O2P O2P
O3P O3P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
CM2 CM2
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
O6 O6
N1 N1
C2 C2
N2 N2
C1M C1M
N3 N3
C4 C4
H2P H2P
H3P H3P
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HA HA
H2'1 1H2*
H2'2 2H2*
HM21 1HM2
HM22 2HM2
HM23 3HM2
H1' H1*
H8 H8
H2N1 1H2N
H2N2 2H2N
H1M1 1H1M
H1M2 2H1M