Atom Nomenclature for MR9

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 MR9

Atom Name (V3) Atom Name (V2)
C26 C26
C27 C27
O3 O3
C28 C28
C29 C29
N6 N6
C20 C20
C21 C21
C22 C22
C23 C23
C25 C25
F2 F2
F3 F3
F1 F1
C24 C24
C19 C19
N4 N4
C17 C17
O2 O2
C12 C12
C11 C11
C13 C13
C14 C14
C15 C15
C16 C16
C10 C10
O1 O1
C9 C9
N3 N3
C8 C8
C7 C7
C6 C6
C5 C5
C2 C2
N1 N1
C3 C3
C4 C4
N2 N2
C1 C1
N5 N5
C18 C18
H261 1H26
H262 2H26
H271 1H27
H272 2H27
H281 1H28
H282 2H28
H291 1H29
H292 2H29
H21 H21
H22 H22
H24 H24
HN4 HN4
H11 H11
H13 H13
H14 H14
H161 1H16
H162 2H16
H163 3H16
H8 H8
H7 H7
H6 H6
H3 H3
H4 H4
HN5 HN5
H181 1H18
H182 2H18
H183 3H18