Atom Nomenclature for NM6

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 NM6

Atom Name (V3) Atom Name (V2)
O4 O4
C3A C3A
C1 C1
C3B C3B
C2 C2
C3C C3C
C3 C3
C4 C4
N3A N3A
O7 OAP
O3B O3B
O3 O3A
C5 C5
C6 C5B
C7 C2A
C8 C2B
N2 N2A
O6 O5B
O5 O6
O1 O1
H4 HAZ
HAQ HAQ
HAT1 HAT1
HAT2 HAT2
HAT3 HAT3
H1 H1A
H2 HAU
HO1 HX0
H3 H3A
HN2 H2N
HAS1 HAS1
HAS2 HAS2
H5 HBA
H61 HBB1
H62 HBB2
HO6 HBC
H81 HBE1
H82 HBE2
H83 HBE3
HO4 H4