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. 2012 Sep 8;40(20):10203–10214. doi: 10.1093/nar/gks845

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — The binding of 5hmU in the active site. (a) In the WT structure, the N-glycosidic bond of the extrahelical nucleotide is cleaved, and a hydroxyl oxygen atom has been attached to the C1′ of the sugar ring (see Figure 3a inset). (b) Favorable face-to-face and edge-to-face hydrophobic interactions between the sugar, the cleaved 5hmU base and Tyr152. (c) Omit electron density, contoured at 3.5σ above the mean, is shown for omitting 5hmU. The hydrogen bond interactions (dashed lines) with the polar atoms of 5hmU are within 3.0 Å distance cutoff: mc, main-chain-atom-mediated contacts. (d) The 5hmU-binding pocket is rich in polar atoms. (e) A hydrogen-bonding network involves both side chain and main chain atoms of depicted residues. The activity of N230D is shown.