Atom Nomenclature for M8F

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 M8F

Atom Name (V3) Atom Name (V2)
C8 C8
O9 O9
O4 O4
C7 C7
C2 C2
C1 C1
C5 C5
C6 C6
N1 N1
O3 O3
N10 N10
C11 C11
C14 C14
O15 O15
C12 C12
S13 S13
N16 N16
C17 C17
C22 C22
O24 O24
C18 C18
C19 C19
S20 S20
C21 C21
O23 O23
H7 H7
H7A H7A
H1 H1
H5 H5
H5A H5A
H6 H6
H6A H6A
HN1 HN1
HN1A HN1A
HO3 HO3
HN10 HN10
H11 H11
H12 H12
H12A H12A
HS13 HS13
HN16 HN16
H17 H17
H18 H18
H18A H18A
H19 H19
H19A H19A
H21 H21
H21A H21A
H21B H21B
HO23 HO23