Atom Nomenclature for DEF

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 DEF

Atom Name (V3) Atom Name (V2)
FE FE
O11 O11
O12 O12
O21 O21
O22 O22
O31 O31
O32 O32
N11 N11
C11 C11
C12 C12
C13 C13
C14 C14
O13 O13
N12 N12
C15 C15
C16 C16
C18 C18
C17 C17
C19 C19
N21 N21
C21 C21
C22 C22
C23 C23
C24 C24
O23 O23
N22 N22
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
N31 N31
C31 C31
C32 C32
C39 C39
C33 C33
C40 C40
C41 C41
C42 C42
C43 C43
N44 N44
O45 O45
S46 S46
O47 O47
O48 O48
C49 C49
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H12N NH12
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H181 1H18
H182 2H18
H171 1H17
H172 2H17
H191 1H19
H192 2H19
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H22N NH22
H251 1H25
H252 2H25
H261 1H26
H262 2H26
H271 1H27
H272 2H27
H281 1H28
H282 2H28
H291 1H29
H292 2H29
H321 1H32
H322 2H32
H391 1H39
H392 2H39
H331 1H33
H332 2H33
H333 3H33
H401 1H40
H402 2H40
H411 1H41
H412 2H41
H421 1H42
H422 2H42
H431 1H43
H432 2H43
H44N NH44
H491 1H49
H492 2H49
H493 3H49