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PDB ID Mentions in PubMed Central Article count: 1

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PDB ID Mentions in PubMed Central

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Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies.

(2008) Nucleic Acids Res 36

PubMed: 18986998 | PubMedCentral: PMC2602767 | DOI: 10.1093/nar/gkn843

The superimposed global and local structures of the 6-Se-G-modified (2R7Y) and native (2G8U) DNA/RNA duplexes (5′-A TGTCG -p-3′/5′-U CGACA -3′) of the nucleic acid... 13;protein complex; the balls represent selenium atoms in the Se-derivatized DNA (5′-AT- Se G-TC- Se G-p-3′).

( A ) The structure of the Se-DNA sequence (2R7Y, in yellow) is superimposed over the corresponding native (2G8U, in grey); ( B ) The structure of the RNA sequence (2R7Y, in green) is superimposed over the corresponding native (2G8U, in grey); ( C ) The duplex structure of the Se-DNA/RNA hybrid (2R7Y, in green) is superimposed over the corresponding native (2G8U, in cyan); ( D ) The comparison of the Se-modified (in green) and native (in cyan) G3/C5 base-pair structures; ( E ) The Se-G3/C5 base pair (2R7Y) with the experimental electron density shows three hydrogen bonds (exo-6-Se/exo-4-NH 2 , 1-NH/N3, and exo-2-NH 2 /exo-2-O) with bond lengths in 3.48 Å, 3.16 Å and 2.59 Å, respectively.

Our study reveals that the protein structures of both the native (2.70 Å resolution, PDB ID: 2G8U; 37,38) and modified (1.80 Å resolution, PDB ID: 2R7Y) complexes are virtually identical, and that the nucleic acid global structures of the native and Se-modified duplexes are very similar ( Figure 6 ) though the nucleobases shift locally ( Figure 6 A–D).

Publication Year: 2008