Atom Nomenclature for 6D0

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 6D0

Atom Name (V3) Atom Name (V2)
O1 O
C1 C
C2 CA
N1 N
C3 CB
C4 CG
N2 NA*
C5 C5*
C6 C4*
O2 O4*
C7 C1*
C8 C2*
O3 O2*
C9 C3*
O4 O3*
N3 N9
C10 C8
N4 N7
C11 C5
C12 C6
N5 N6
C13 C4
N6 N3
C14 C2
N7 N1
C15 CB*
C16 CG*
C17 CD*
O5 OD1*
BR1 BRE*
O6 OXT
H1 HA
H2 H2
H3 H
H5 HB2
H6 HB3
H7 HG3
H8 HG2
H10 H5*1
H11 H5*2
H12 H4*1
H13 H1*1
H14 H2*1
H15 H2*2
H16 H3*1
H17 H3*2
H18 H81
H19 H62
H20 H61
H21 H21
H22 HB*2
H23 HB*1
H24 HD*2
H25 HD*1
H26 H4