Atom Nomenclature for 0EF

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 0EF

Atom Name (V3) Atom Name (V2)
O1 O1
C C1
O2 O2
CT C2
C1 C3
C2 C4
C3 C5
N N1
CA C6
C4 C7
O O4
CB C8
N1 N2
CA1 C9
C5 C10
O3 O6
CB1 C11
CG C12
CD C13
N2 N3
CA2 C14
CB2 C15
CG1 C16
CD1 C17
CD2 C18
CE1 C19
CE2 C20
CZ C21
NHO N4
C6 C22
O4 O8
OXT O9
H11 H1
H12 H2
H13 H3
H21 H4
H22 H5
H23 H6
H31 H7
H32 H8
H33 H9
H H11
HA H13
HB1 H14
HB2 H15
HB3 H16
HA1 H19
HB21 H20
HB31 H21
HG2 H22
HG3 H23
HD2 H24
HD3 H25
H1 H27
HA2 H29
HB22 H30
HB32 H31
HD1 H32
HD21 H33
HE1 H34
HE2 H35
HZ H36
HN H37
HXT H38