Atom Nomenclature for ZPN

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 ZPN

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
C3 C3
C4 C4
C5 C5
C21 C21
C6 C6
C7 C7
O7 O7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C22 C22
C14 C14
C15 C15
O11 O11
C16 C16
C17 C17
C23 C23
C18 C18
C19 C19
O19 O19
C20 C20
O20 O20
N20 N20
C1' C1'
O1' O1'
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
H21 H21
H31 H31
H41 H41
H211 H211
H212 H212
H213 H213
H62 H62
H61 H61
H81 H81
H82 H82
H91 H91
H92 H92
H102 H102
H162 H162
H141 H141
H151 H151
H142 H142
H223 H223
H222 H222
H121 H121
H122 H122
H111 H111
H101 H101
H231 H231
H232 H232
H233 H233
H181 H181
H182 H182
H191 H191
H201 H201
H202 H202
H203 H203
H2'1 H2'1
H3'1 H3'1
H4'1 H4'1
H6 H6
H7 H7
H8 H8
H9 H9