Atom Nomenclature for GZZ

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 GZZ

Atom Name (V3) Atom Name (V2)
NH1 NH1
NH2 NH2
CZ1 CZ1
NE1 NE1
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
N9 N9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
NE2 NE2
CZ2 CZ2
NH3 NH3
NH4 NH4
HHN1 HHN1
HH21 1HH2
HH22 2HH2
HN1E EHN1
HC11 1HC1
HC12 2HC1
HC21 1HC2
HC22 2HC2
HC31 1HC3
HC32 2HC3
HC41 1HC4
HC42 2HC4
HC51 1HC5
HC52 2HC5
HC61 1HC6
HC62 2HC6
HC71 1HC7
HC72 2HC7
HC81 1HC8
HC82 2HC8
HN9 9HN
H101 1H10
H102 2H10
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
HN2E EHN2
HH31 1HH3
HH32 2HH3
HHN4 HHN4