Atom Nomenclature for ZOZ

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 ZOZ

Atom Name (V3) Atom Name (V2)
OAP OAP
CAP CAP
C9P C9P
O9P O9P
N8P N8P
C7P C7P
C6P C6P
C5P C5P
O5P O5P
N4P N4P
C3P C3P
C2P C2P
S1P S1P
C1' C1'
O1' O1'
C2' C2'
C3' C3'
O3' O3'
C4' C4'
C5' C5'
C6' C6'
C7' C7'
C8' C8'
C9' C9'
C10 C10
CBP CBP
CDP CDP
CEP CEP
CCP CCP
O6A O6A
P2A P2A
O4A O4A
O5A O5A
O3A O3A
P1A P1A
O1A O1A
O2A O2A
O5B O5B
C5B C5B
C4B C4B
O4B O4B
C1B C1B
N9A N9A
C8A C8A
N7A N7A
C5A C5A
C4A C4A
N3A N3A
C2A C2A
N1A N1A
C6A C6A
N6A N6A
C2B C2B
O2B O2B
C3B C3B
O3B O3B
P3B P3B
O9A O9A
O8A O8A
O7A O7A
HAP HAP
HA HA
H8P H8P
H7P1 H7P1
H7P2 H7P2
H6P1 H6P1
H6P2 H6P2
H4P H4P
H3P1 H3P1
H3P2 H3P2
H2P1 H2P1
H2P2 H2P2
H2'1 H2'1
H2'2 H2'2
H4'1 H4'1
H4'2 H4'2
H5'1 H5'1
H5'2 H5'2
H6'1 H6'1
H6'2 H6'2
H7'1 H7'1
H7'2 H7'2
H8'1 H8'1
H8'2 H8'2
H9'1 H9'1
H9'2 H9'2
H101 H101
H102 H102
H103 H103
HDP1 HDP1
HDP2 HDP2
HDP3 HDP3
HEP1 HEP1
HEP2 HEP2
HEP3 HEP3
HCP1 HCP1
HCP2 HCP2
H5A H5A
H1A H1A
H5B1 H5B1
H5B2 H5B2
H4B H4B
H3B H3B
H1B H1B
H2B H2B
H8A H8A
H2A H2A
H6A1 H6A1
H6A2 H6A2
HB HB
H9A H9A
H7A H7A