Atom Nomenclature for 6J2

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 6J2

Atom Name (V3) Atom Name (V2)
C3I C11
O3I O7
C1I C12
C2I C13
O3P O8
P P1
O1P O9
O2P O10
O5' O11
C5' C14
C4' C15
O4' O12
C3' C16
O3' O13
C2' C17
O2' O14
C1' C18
N10 N4
C9A C19
C9 C20
C8 C21
O8M O15
C7 C22
C6 C23
C5A C24
C5 C25
C10 C26
N1 N5
C4A C27
C4 C28
O4 O16
N3 N6
C2 C29
O2 O17
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H37 H37
OXT OXT
HXT HXT