Atom Nomenclature for RX6

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 RX6

Atom Name (V3) Atom Name (V2)
C1 C1
N1 N1
O1 O1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
CL28 CL28
C32 C32
C33 C33
C34 C34
N35 N35
O35 O35
C36 C36
C37 C37
C38 C38
C39 C39
C40 C40
N42 N42
C43 C43
O44 O44
N45 N45
C46 C46
C47 C47
C48 C48
C49 C49
C50 C50
C51 C51
CT2 CT2
CT3 CT3
H1 H1
HN1 HN1
H2 H2
H2A H2A
H2B H2B
H4 H4
H5 H5
H7 H7
H8 H8
H32 H32
H33 H33
H33A H33A
H34 H34
H34A H34A
HN35 HN35
H36 H36
H37 H37
H37A H37A
H38 H38
H38A H38A
H39 H39
H39A H39A
H40 H40
H40A H40A
HN42 HN42
H46 H46
H46A H46A
H47 H47
H47A H47A
H48 H48
H49 H49
H49A H49A
H50 H50
H50A H50A
H51 H51
H51A H51A
H51B H51B
HT2 HT2
HT2A HT2A
HT3 HT3
HT3A HT3A