Atom Nomenclature for C3S

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 C3S

Atom Name (V3) Atom Name (V2)
C65 C65
C63 C63
C69 C69
C60 C60
C57 C57
C54 C54
C48 C48
C50 C50
C38 C38
C35 C35
C29 C29
C26 C26
C40 C40
C30 C30
C32 C32
C18 C18
C15 C15
C20 C20
C23 C23
C22 C22
C44 C44
C12 C12
C9 C9
C13 C13
C1 C1
C4 C4
C7 C7
O6 O6
S1 S1
O3 O3
O2 O2
O4 O4
H651 1H65
H652 2H65
H653 3H65
H63 H63
H691 1H69
H692 2H69
H693 3H69
H601 1H60
H602 2H60
H571 1H57
H572 2H57
H541 1H54
H542 2H54
H48 H48
H501 1H50
H502 2H50
H503 3H50
H38 H38
H351 1H35
H352 2H35
H261 1H26
H262 2H26
H401 1H40
H402 2H40
H403 3H40
H30 H30
H321 1H32
H322 2H32
H18 H18
H151 1H15
H152 2H15
H20 H20
H231 1H23
H232 2H23
H441 1H44
H442 2H44
H443 3H44
H91 1H9
H92 2H9
H13 H13
H11 1H1
H12 2H1
H41 1H4
H42 2H4
H7 H7
HO3 HO3