3QK4
Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex
Summary for 3QK4
| Entry DOI | 10.2210/pdb3qk4/pdb |
| Descriptor | DNA (5'-D(*CP*GP*CP*GP*GP*GP*TP*AP*CP*CP*CP*GP*CP*G)-3') (2 entities in total) |
| Functional Keywords | a-dna duplex, dna |
| Total number of polymer chains | 2 |
| Total formula weight | 8565.54 |
| Authors | Venkadesh, S.,Mandal, P.K.,Gautham, N. (deposition date: 2011-01-31, release date: 2011-03-02, Last modification date: 2024-04-03) |
| Primary citation | Venkadesh, S.,Mandal, P.K.,Gautham, N. The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2) Biochem.Biophys.Res.Commun., 407:307-312, 2011 Cited by PubMed Abstract: We report the 2.6Å resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4₃. This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours. PubMed: 21397589DOI: 10.1016/j.bbrc.2011.03.007 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.6 Å) |
Structure validation
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