Atom Nomenclature for X85

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 X85

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
N8 N8
O9 O9
N10 N10
O11 O11
O12 O12
N13 N13
C14 C14
N15 N15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
N21 N21
C22 C22
C23 C23
O24 O24
C25 C25
N26 N26
C27 C27
C28 C28
C29 C29
C30 C30
H1 H1
H4 H4
H1N8 H1N8
H2N8 H2N8
HN13 HN13
H114 H114
H214 H214
HN15 HN15
H116 H116
H216 H216
H117 H117
H217 H217
H118 H118
H218 H218
H119 H119
H219 H219
H120 H120
H220 H220
H122 H122
H222 H222
H123 H123
H223 H223
H25 H25
H27 H27
H29 H29
H30 H30