Atom Nomenclature for TZ5

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 TZ5

Atom Name (V3) Atom Name (V2)
N2 N2
C8 C8
C7 C7
C6 C6
C5 C5
C19 C19
C18 C18
N3 N3
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C10 C10
C9 C9
C4 C4
C3 C3
C2 C2
C1 C1
N1 N1
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
N4 N4
N5 N5
N6 N6
C27 C27
C28 C28
C29 C29
N7 N7
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
N8 N8
C37 C37
C38 C38
C39 C39
C40 C40
C41 C41
C42 C42
HN21 1HN2
HN22 2HN2
H7 H7
H6 H6
H19 H19
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H9 H9
H3 H3
H2 H2
HN11 1HN1
HN12 2HN1
H201 1H20
H202 2H20
H211 1H21
H212 2H21
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H241 1H24
H242 2H24
H251 1H25
H252 2H25
H27 H27
H281 1H28
H282 2H28
H291 1H29
H292 2H29
HN7 HN7
H32 H32
H34 H34
H35 H35
H36 H36
H381 1H38
H382 2H38
H401 1H40
H402 2H40
H411 1H41
H412 2H41
H421 1H42
H422 2H42