Atom Nomenclature for CY6

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 CY6

Atom Name (V3) Atom Name (V2)
C5 C5
C6 C6
O7 O7
N8 N8
C9 C9
C10 C10
C11 C11
O12 O12
N13 N13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
O19 O19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C29 C29
O30 O30
N31 N31
C32 C32
C33 C33
C34 C34
C35 C35
O36 O36
O37 O37
C38 C38
C39 C39
C40 C40
C41 C41
C42 C42
C43 C43
N44 N44
C45 C45
O46 O46
H51 1H5
H52 2H5
H53 3H5
H10 H10
H13 H13
H14 H14
H15 H15
H161 1H16
H162 2H16
H163 3H16
H171 1H17
H172 2H17
H173 3H17
H201 1H20
H202 2H20
H21 H21
H221 1H22
H222 2H22
H23 H23
H251 1H25
H252 2H25
H253 3H25
H261 1H26
H262 2H26
H263 3H26
H31 H31
H32 H32
H33 H33
H34 H34
H381 1H38
H382 2H38
H391 1H39
H392 2H39
H393 3H39
H401 1H40
H402 2H40
H41 H41
H421 1H42
H422 2H42
H431 1H43
H432 2H43
H44 H44