Atom Nomenclature for 5HA

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 5HA

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
N1 N1
C4 C4
C5 C5
C6 C6
N2 N2
C7 C7
O2 O2
O3 O3
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
N3 N3
O4 O4
C16 C16
S1 S1
C23 C23
O5 O5
O6 O6
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
N4 N4
C17 C17
C18 C18
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
H11 1H1
H12A 2H1
H2 H2
H31A 1H3
H32A 2H3
HN1 HN1
H41 1H4
H42 2H4
H5 H5
H6 H6
HN2 HN2
HO3 HO3
H81 1H8
H82 2H8
H10 H10
H12 H12
H14 H14
H161 1H16
H162 2H16
H163 3H16
H231 1H23
H232 2H23
H233 3H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
HN4 HN4
H17 H17
H181 1H18
H182 2H18
H183 3H18
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35