Atom Nomenclature for MY6

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 MY6

Atom Name (V3) Atom Name (V2)
C1 C1
N2 N2
C3 C3
N4 N4
C5 C5
C6 C6
O7 O7
N8 N8
C9 C9
N10 N10
N11 N11
C12 C12
H1 H1
H1A H1A
H1B H1B
H3 H3
HN8 HN8
HN10 HN10
HN1A HN1A