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Figure 5
Comparison of the anaerobic and O2-exposed AlkB structures. (a) Structural overview of the anaerobic AlkB:Fe:2OG:T-1-meA-T complex structure (PDB entry 6y0q, this study). (b) Composite omit map to 1.75 Å resolution of the active site carved around the methyl­ated DNA fragment displayed at 1.0σ contour level. (c) Superimposition of the cryogenic AlkB:Fe:2OG:T-1-meA-T complex [magenta and salmon, PDB entry 2fd8 (Yu et al., 2006BB66)] and the serial RT structure reported here (cyan and yellow, PDB entry 6y0q). (d) Fobs − Fobs isomorphous difference maps carved around the methyl­ated DNA fragment contoured at +2.0σ (green) and −2.0σ (red) for the AlkB:Fe:2OG structure [PDB entry 6ypv (this study)] relative to the AlkB:Fe:2OG:T-1-meA-T structure (PDB entry 6y0q).

IUCrJ
Volume 7| Part 5| September 2020| Pages 901-912
ISSN: 2052-2525
https://doi.org/10.1107/S2052252520010374