Atom Nomenclature for 3CY

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 3CY

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
S1 S1
C8 C8
C9 C9
C10 C10
O1 O1
N1 N1
C11 C11
C12 C12
O2 O2
O3 O3
C13 C13
O4 O4
C21 C21
N2 N2
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C22 C22
C23 C23
C24 C24
C25 C25
O5 O5
N3 N3
C26 C26
C27 C27
O6 O6
N4 N4
C30 C30
C31 C31
O9 O9
C28 C28
C29 C29
O8 O8
O7 O7
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H71 1H7
H72 2H7
H81 1H8
H82 2H8
H10 H10
HN1 HN1
H111 1H11
H112 2H11
HO3 HO3
H14 H14
H151 1H15
H152 2H15
H17 H17
H18 H18
H19 H19
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H24 H24
HN3 HN3
H27 H27
HN4 HN4
H311 1H31
H312 2H31
H313 3H31
H281 1H28
H282 2H28
HO8 HO8