Atom Nomenclature for CC0

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 CC0

Atom Name (V3) Atom Name (V2)
P1 P1
OR1 OR1
OR2 OR2
O10 O10
C1 C1
N1 N1
C0 C0
C3 C3
O2 O2
N2 N2
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
O3 O3
C11 C11
C12 C12
C13 C13
O4 O4
O5 O5
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
N3 N3
O6 O6
C28 C28
C29 C29
O7 O7
O8 O8
HR1 HR1
H10 H10
HC11 1HC1
HN11 1HN1
HC01 1HC0
HN21 1HN2
HC41 1HC4
HC42 2HC4
HC61 1HC6
HC71 1HC7
HC91 1HC9
H111 1H11
H112 2H11
H113 3H11
H131 1H13
H132 2H13
H133 3H13
H151 1H15
H181 1H18
H191 1H19
H201 1H20
H202 2H20
H211 1H21
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H241 1H24
H242 2H24
H251 1H25
H252 2H25
H261 1H26
H262 2H26
HN31 1HN3
HN32 2HN3
H281 1H28
H282 2H28
HXT HXT