Atom Nomenclature for CEH

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 CEH

Atom Name (V3) Atom Name (V2)
S1 S1
C1 C1
C2 C2
C3 C3
N1 N1
C4 C4
C5 C5
C6 C6
O1 O1
O2 O2
O3 O3
N2 N2
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
O11 O11
C17 C17
C18 C18
C19 C19
N4 N4
O4 O4
N3 N3
C24 C24
O7 O7
C20 C20
C25 C25
C27 C27
C28 C28
C29 C29
O8 O8
N6 N6
C30 C30
C31 C31
O9 O9
O10 O10
C21 C21
C22 C22
C23 C23
N5 N5
C26 C26
O5 O5
O6 O6
O13 O13
C32 C32
O12 O12
H11 1H1
H12A 2H1
HN1 HN1
H4 H4
H51 1H5
H52 2H5
HO2 HO2
HN2 HN2
H7 H7
H101 1H10
H102 2H10
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H171 1H17
H172 2H17
H18 H18
HN4 HN4
HN3 HN3
H201 1H20
H202 2H20
H251 1H25
H252 2H25
H253 3H25
H27 H27
H281 1H28
H282 2H28
H283 3H28
HN6 HN6
H30 H30
HO10 HO10
H211 1H21
H212 2H21
H22 H22
HN5 HN5
HO5 HO5
HO13 HO13
H321 1H32
H322 2H32
H323 3H32