Atom Nomenclature for CXE

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 CXE

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
O11 O11
C12 C12
C13 C13
O14 O14
C15 C15
C16 C16
O17 O17
C18 C18
C19 C19
O20 O20
C21 C21
C22 C22
O23 O23
C24 C24
C25 C25
O26 O26
H011 1H01
H012 2H01
H013 3H01
H021 1H02
H022 2H02
H031 1H03
H032 2H03
H041 1H04
H042 2H04
H051 1H05
H052 2H05
H061 1H06
H062 2H06
H071 1H07
H072 2H07
H081 1H08
H082 2H08
H091 1H09
H092 2H09
H101 1H10
H102 2H10
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H181 1H18
H182 2H18
H191 1H19
H192 2H19
H211 1H21
H212 2H21
H221 1H22
H222 2H22
H241 1H24
H242 2H24
H251 1H25
H252 2H25
H26 H26