Atom Nomenclature for 2YB

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 2YB

Atom Name (V3) Atom Name (V2)
C4 C1
C6 C2
C7 C3
C8 C4
C10 C5
C13 C6
C15 C7
C17 C8
C20 C9
C21 C10
C22 C11
C24 C12
C26 C13
C28 C14
C1 C15
C2 C16
C3 C17
O5 O1
S9 S1
O11 O2
O12 O3
C14 C18
C16 C19
C18 C20
C19 C21
O23 O4
C25 C22
C27 C23
C30 C24
C31 C25
O32 O5
O33 O6
C34 C26
O35 O7
C36 C27
C37 C28
C38 C29
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
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