Atom Nomenclature for Z34

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 Z34

Atom Name (V3) Atom Name (V2)
C1 C1
F1 F1
C2 C2
C3 C3
F2 F2
C4 C4
N5 N5
C6 C6
O11 O11
O1 O1
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
N11 N11
N12 N12
O2 O2
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
N21 N21
C30 C30
N22 N22
C28 C28
C29 C29
N31 N31
C32 C32
C33 C33
O34 O34
O35 O35
C36 C36
H11 H11
H12 H12
H14 H14
H15 H15
H111 1H11
H121 1H12
H122 2H12
H22 H22
H23 H23
H24 H24
H26 H26
H301 1H30
H302 2H30
H303 3H30
H281 1H28
H282 2H28
H291 1H29
H292 2H29
H321 1H32
H322 2H32
H35 H35
H361 1H36
H362 2H36
H363 3H36