Atom Nomenclature for MBP

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 MBP

Atom Name (V3) Atom Name (V2)
C2 C2
C4 C4
C5 C5
C4' C4*
O4' O4*
C3' C3*
C2' C2*
C12 C12
N9 N9
N3 N3
N2 N2
N1 N1
C6 C6
O6 O6
C60 C60
N7 N7
C8 C8
H3'1 1H3*
H3'2 2H3*
H3'3 3H3*
H2' H2*
H121 1H12
H122 2H12
H123 3H12
H2N1 1H2N
H2N2 2H2N
H601 1H60
H602 2H60
H7 H7
H8 H8