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Figure 2
Natural CPD binding by MmCPDII. (a) Determining the nature of the CPD backbone. Electron density for PDM (blue; PDB entry 5zcw) was much more prominent than for FDM (red; PDB entry 2xrz), clearly confirming the presence of a phosphodiester backbone. Electron densities were calculated as OMIT maps at a 1.5σ contour level against their respective models and then superposed with the PDM structure. (b) The PDM active site. The active site of the co-crystal structure contained the CPD (bright green) as well as an oxidized FAD cofactor (gold). It also included the class II CPD photolyase-specific water cluster (6WC). (c) Stabilizing the distorted DNA in the presence of a native CPD. Superposition of the active-site residues of PDM (green) and FDM (pale blue) reveals an ∼15° twist in the DNA geometry, which is accompanied by side-chain and base rearrangements (black arrows). Furthermore, the immediate hydration sphere also shifts, facilitating new interactions (WA1, WA2 and WA3 in red for PDM and in pale blue for FDM). (d) The lock bolt of the BIR. Top, the BIR lock bolt in the presence of a phosphodiester-linked CPD lesion (PDB entry 5zcw). The differential locking interaction between Asp428 and Trp431 is highlighted in red. Bottom, the BIR lock bolt in the presence of a formacetal-linked CPD lesion (PDB entry 2xrz).

IUCrJ
Volume 5| Part 5| September 2018| Pages 608-618
ISSN: 2052-2525
https://doi.org/10.1107/S205225251800996X