Fig. 7

Movement of Arg167 in the D4:DNA complex and A20 binding. a. Arg167 side chain of D4 in the DNA complex and in DNA-free D4. Stereo diagram showing movement of Arg167 and Pro173 residues of D4 chains A and B in the DNA complex (shown in blue and purple violet colors) superimposed on D4 subunits in different subunits of the uracil complex (4lzb) shown in various shades of yellow and green. Arg167 and Pro173 residues are shown in stick model. b. Hydrogen bonding interactions of Arg167 in the DNA complex. Close up view of the above region showing hydrogen bonding interactions of Arg167 of the two D4 chains A and B of the DNA complex in the left and right panel, respectively. c. Orientations of Arg167 and Pro173 in the DNA complex. Cartoon drawing showing close up view of the A20 binding site on D4. D4 subunits from free-D4 (4dof subunit A, white), and D4 subunits A and B from the DNA complex (cyan and marine) are superimposed on the D4 subunit of the D4:A20 complex (4od8, yellow). The A20 molecule in 4od8 is colored in wheat. Trp43 and Lys44 residues of A20 are shown in stick model (carbon atoms in orange). Arg167 residues of D4 chains are also shown in stick models and carbon atoms of each stick model are colored according to the chain. Orientations of Arg167 and Pro173 of the D4 subunits in the DNA complex are unfavorable for binding of A20 in the groove