2FII
Crystal Structure Analysis of the B-DNA Dodecamer CGCGAAT-aU-CGCG, with Incorporated Arabino-Uridin (aU)
Summary for 2FII
| Entry DOI | 10.2210/pdb2fii/pdb |
| Related | 2FIH 2FIJ 2FIL |
| Descriptor | 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UAR)P*CP*GP*CP*G)-3', MAGNESIUM ION (3 entities in total) |
| Functional Keywords | arabinonucleic acid, sugar modifications, b-form dna, dna |
| Total number of polymer chains | 2 |
| Total formula weight | 7355.03 |
| Authors | |
| Primary citation | Li, F.,Sarkhel, S.,Wilds, C.J.,Wawrzak, Z.,Prakash, T.P.,Manoharan, M.,Egli, M. 2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H. Biochemistry, 45:4141-4152, 2006 Cited by PubMed Abstract: 2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A- and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A- and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity. PubMed: 16566588DOI: 10.1021/bi052322r PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.24 Å) |
Structure validation
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