1VTT

GT Wobble Base-Pairing in Z-DNA at 1.0 Angstrom Atomic Resolution: The Crystal Structure of d(CGCGTG)

Summary for 1VTT

• Entry DOI: 10.2210/pdb1vtt/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3') (1 entity in total)
• Functional Keywords: z-dna, double helix, mismatched, dna
• Total number of polymer chains: 2
• Total formula weight: 3650.43

Authors

Ho, P.S.,Frederick, C.A.,Quigley, G.J.,Van Der Marel, G.A.,Van Boom, J.H.,Wang, A.H.-J.,Rich, A. (deposition date: 1988-08-18, release date: 2011-07-13, Last modification date: 2023-12-27)

Primary citation

Ho, P.S.,Frederick, C.A.,Quigley, G.J.,Van Der Marel, G.A.,Van Boom, J.H.,Wang, A.H.-J.,Rich, A.
GT Wobble Base-Pairing in Z-DNA at 1.0 Angstrom Atomic Resolution: The Crystal Structure of d(CGCGTG)
Embo J., 4:3617-3623, 1985

PubMed Abstract: The DNA oligomer d(CGCGTG) crystallizes as a Z-DNA double helix containing two guanine-thymine base pair mismatches of the wobble type. The crystal diffracts to 1 A resolution and the structure has been solved and refined. At this resolution, a large amount of information is revealed about the organization of the water molecules in the lattice generally and more specifically around the wobble base pairs. By comparing this structure with the analogous high resolution structure of d(CGCGCG) we can visualize the structural changes as well as the reorganization of the solvent molecules associated with wobble base pairing. There is only a small distortion of the Z-DNA backbone resulting from introduction of the GT mismatched base pairs. The water molecules cluster around the wobble base pair taking up all of the hydrogen bonding capabilities of the bases due to wobble pairing. These bridging water molecules serve to stabilize the base-base interaction and, thus, may be generally important for base mispairing either in DNA or in RNA molecules.

PubMed: 4092690

Experimental method

X-RAY DIFFRACTION (1 Å)