1G8U

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA

Summary for 1G8U

• Entry DOI: 10.2210/pdb1g8u/pdb
• Descriptor: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UFR)P*CP*GP*CP*G)-3' (2 entities in total)
• Functional Keywords: modified nucleotide, formyluridine, dna damage, b-dna, double helix, deoxyribonucleic acid, dna
• Total number of polymer chains: 2
• Total formula weight: 7354.75

Authors

Tsunoda, M.,Karino, N.,Ueno, Y.,Matsuda, A.,Takenaka, A. (deposition date: 2000-11-21, release date: 2001-02-05, Last modification date: 2023-08-09)

Primary citation

Tsunoda, M.,Karino, N.,Ueno, Y.,Matsuda, A.,Takenaka, A.
Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?
Acta Crystallogr.,Sect.D, 57:345-348, 2001

PubMed Abstract: To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2'-deoxy-5-formyluridine at X, were obtained under several conditions with and without divalent cations. The crystal structures are all isomorphous. The octahedrally hydrated magnesium cations found in the major groove cement the two neighbouring duplexes along the b axis. In the Mg(2+)-free crystals, a five-membered ring of water molecules occupies the same position as the magnesium site and connects the two duplexes similarly to the hydrated Mg(2+) ion. It has been concluded that water molecules can take the place of the hydrated magnesium cation in crystallization, but the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution. In all four crystals, the 5-formyluracil residues form the canonical Watson-Crick pair with adenine residues.

PubMed: 11173500
DOI: 10.1107/S0907444900017583

Experimental method

X-RAY DIFFRACTION (1.85 Å)