2B1B: 5'-d(*gp*cp*gp*tp*gp*gp*gp*cp*ap*c)-3' Zif268 Binding Site

One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel beta strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition.
PDB ID: 2B1BDownload
MMDB ID: 52546
PDB Deposition Date: 2005/9/15
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Biological Unit for 2B1B: dimeric; determined by author
Molecular Components in 2B1B
Label Count Molecule
Nucleotides(2 molecules)
Molecule annotation
Molecule annotation
Chemical (1 molecule)
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Citing MMDB