Atom Nomenclature for ZP4

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 ZP4

Atom Name (V3) Atom Name (V2)
O5' O5'
N3' N3'
N3A N3A
N3B N3B
N1 N1
C6 C6
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C5A C5A
C2' C2'
C5' C5'
C4' C4'
O4' O4'
C1' C1'
C3' C3'
PA PA
O1A O1A
O2A O2A
O3A O3A
PB PB
O1B O1B
O2B O2B
O3B O3B
PG PG
O1G O1G
O2G O2G
O3G O3G
PD PD
O1D O1D
O2D O2D
O51 O51
C51 C51
C41 C41
O41 O41
C11 C11
C21 C21
O21 O21
C31 C31
O31 O31
N9R N9R
C8R C8R
N7R N7R
C5R C5R
C6R C6R
N6R N6R
N1R N1R
C2R C2R
N3R N3R
C4R C4R
H6 H6
HN3 HN3
H5A H5A
H5AA H5AA
H5AB H5AB
H2' H2'
H2'A H2'A
H5' H5'
H5'A H5'A
H4' H4'
H1' H1'
H3' H3'
HO1A HO1A
HO1B HO1B
HO2G HO2G
HO1D HO1D
H51 H51
H51A H51A
H41 H41
H11 H11
H21 H21
HO21 HO21
H31 H31
HO31 HO31
H8R H8R
HN6R HN6R
HN6A HN6A
H2R H2R