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. 2013 Aug 8;9(8):e1003160. doi: 10.1371/journal.pcbi.1003160

Figure 5. Contacts by helix 3 in the major groove of Conformation B during the solution simulation.

Figure 5

A) Ribbon diagram looking into helix 3 and the major groove. Asn 51 contacts Ade 3 directly (blue dotted line). Gln 50 makes no direct contact with the DNA. About 20% of the time, water mediated contacts bridge between Gln 50 and Asn 51 (W1) and Gln 50 and DNA bases (in green) (W2). Distances show helix 3 binds farther in the major groove (Asn 51 C-alpha to Ade 3 N7 distance 6.15 Å), and the major groove is slightly wider than in Conformation A (Thy 1 P – Cyt 7* P distance 19.9 Å). B) Asn 51 forms a direct hydrogen bond with the base Ade 3 N7 only in Conformation B (red), not in Conformation A (black). C) and D) The position of the homeodomain differs in Conformation A and Conformation B during the solution simulation. C) Helix 3 binds closer to the DNA in Conformation B (red) than Conformation A (black), as measured by the distance between Asn 51 and Ade 3. D) The major groove is wider in Conformation B than Conformation A during most of the solution simulation, as measured by the Cyt 7* P-Thy 1 P distance. This is consistent with Pdx1 binding deeper in the DNA major groove in Conformation B.