Atom Nomenclature for U3S

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 U3S

Atom Name (V3) Atom Name (V2)
C4 C4
C5 C5
C6 C6
N1 N1
N3 N3
CAV CAV
CAK CAK
CAM CAM
CAJ CAJ
CAL CAL
NBA NBA
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
O2' O2'
C1' C1'
O4 O4
C2 C2
O2 O2
H5 H5
H6 H6
HN3 HN3
HAV HAV
HAVA HAVA
HAK HAK
HAKA HAKA
HAM HAM
HAMA HAMA
HAJ HAJ
HAJA HAJA
HAL HAL
HALA HALA
H5' H5'
H5'A H5'A
H4' H4'
H3' H3'
HO3' HO3'
H2' H2'
HO2' HO2'
H1' H1'