The Half–Tyr site of S1 nuclease and the proposed binding of ssDNA.

<p><b>(a)</b> 2'–deoxycytidine (shown as sticks, carbon–magenta) bound in the Half–Tyr site and comparison of the position of the Half–Tyr site of S1 nuclease (carbon–green) with the position of the Tyr site of P1 nuclease (carbon–dark blue) and with respect to the active site. Both secondary sites are positioned at the same end of the active site cleft, albeit on the opposite “banks”. Superposition of the complexes 5FBG–mutant with products, chain A, 5FBF–nuclease products, and of P1 nuclease (PDB ID: 1AK0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168832#pone.0168832.ref011" target="_blank">11</a>]) was calculated using the SSM Superpose tool in <i>Coot</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168832#pone.0168832.ref019" target="_blank">19</a>]. Residues forming the Half–Tyr site are shown as sticks (carbon–green) and labelled. Residues of P1 nuclease involved in the formation of the Tyr site are shown as sticks (carbon–dark blue) and not labelled. The catalytic zinc ions (light blue spheres) with the phosphate ion (red/orange sticks) inside the zinc cluster are shown only for S1 nuclease. NBS1 is not shown but its position is marked. 2'–deoxycytidine and 5’dCMP binding in the active site cleft are shown (carbon–grey). <b>(b)</b> The proposed binding mode of ssDNA in the active site cleft based on the observed interactions of nucleotides and nucleosides in the S1 nuclease structures. The placement of the five nucleotides is based on x–ray structure coordinates except for the two nucleotides shown in green, which were positioned manually with optimized chain geometry in order to demonstrate the possible direction of ssDNA binding. Molecular graphics were created using <i>PyMOL</i> (Schrödinger, LLC).