Atom Nomenclature for 321

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 321

Atom Name (V3) Atom Name (V2)
O31 O31
S35 S35
O30 O30
C19 C19
N26 N26
C8 C8
C3 C3
C5 C5
C9 C9
S34 S34
O28 O28
O29 O29
C11 C11
C14 C14
N24 N24
C7 C7
C2 C2
C13 C13
C15 C15
O32 O32
C16 C16
O27 O27
N25 N25
C21 C21
C20 C20
C22 C22
C18 C18
C17 C17
N23 N23
C12 C12
C10 C10
C4 C4
S33 S33
C6 C6
C1 C1
H19 H19
H19A H19A
H19B H19B
HN26 HN26
H3 H3
H5 H5
H11 H11
H11A H11A
H2 H2
HO32 HO32
H21 H21
H21A H21A
H20 H20
H20A H20A
H22 H22
H18 H18
H18A H18A
H18B H18B
H17 H17
H17A H17A
H17B H17B
H4 H4
H6 H6
H1 H1