Atom Nomenclature for HYF

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 HYF

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
O8 O8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
O19 O19
O20 O20
O21 O21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
H021 1H02
H022 2H02
H023 3H02
H031 1H03
H032 2H03
H033 3H03
H041 1H04
H042 2H04
H043 3H04
H051 1H05
H061 1H06
H062 2H06
H063 3H06
H091 1H09
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H123 3H12
H131 1H13
H132 2H13
H133 3H13
H141 1H14
H142 2H14
H143 3H14
H161 1H16
H171 1H17
H172 2H17
H211 1H21
H221 1H22
H222 2H22
H223 3H22
H231 1H23
H232 2H23
H233 3H23
H251 1H25
H261 1H26
H262 2H26
H321 1H32
H322 2H32
H331 1H33
H351 1H35
H352 2H35
H361 1H36
H362 2H36
H371 1H37
H381 1H38
H382 2H38
H383 3H38
H391 1H39
H392 2H39
H393 3H39