Volume 9, Issue 1, Pages 187-194 (January 2002) Structure of Ocr from Bacteriophage T7, a Protein that Mimics B-Form DNA  M.D Walkinshaw, P Taylor, S.S Sturrock, C Atanasiu, T Berge, R.M Henderson, J.M Edwardson, D.T.F Dryden  Molecular Cell  Volume 9, Issue 1, Pages 187-194 (January 2002) DOI: 10.1016/S1097-2765(02)00435-5

Figure 1 The X-Ray Crystallographic Structure of Ocr (A) A typical portion of the 2Fo–Fc electron density map contoured at 1.5 σ. (B) Stereo view of the ocr dimer. Residues defining the first and last residues of the four helices are labeled: Helix A (Y7 to Y24), Helix B (H34 to A44), Helix C (Y49 to M56), and Helix D (V77 to L105). The crystallographic 2-fold axis relating the two subunits of the dimer (colored red and blue) lies in the plane of the paper. The side chains of the six residues involved in van der Waals contacts between the dimer subunits are shown (Ala50, Phe53, Ser54, Met56, Ala57, and Val77). (C) Stereo view of the ocr dimer (rotated 90° with respect to [B]). Annotation is the same as in (B). The 2-fold axis points into the plane of the paper. The six residues forming the hydrophobic interface are located mainly on helix C. (D) The dimer interface. The view of the interface is along the 2-fold axis (as in [C]). The complementarity of shape of the two subunits (colored blue and red) is depicted by the dotted Connolly surface. Five of the six residues within van der Waals contact distance are shown. Molecular Cell 2002 9, 187-194DOI: (10.1016/S1097-2765(02)00435-5)

Figure 2 DNA Bending Induced by Specific Binding of EcoKI as Visualized Using Atomic Force Microscopy (A) The histogram shows the distributions of bend angles for DNA with specifically bound EcoKI enzyme complexes. Only complexes containing EcoKI located in the center of the DNA fragment were considered. EcoKI was found to induce bending by 46° ± 2° (n = 150) (mean ± standard error). (B) The histogram shows the distribution of bend angles for naked DNA fragments. These were nominally straight over the same region as occupied by EcoKI with a distribution mean of 0° ± 3° (n = 50). The distributions are truncated at 0°, as the direction of the bending was not determined. (C–E) AFM images of specifically bound EcoKI complexes on 292 bp DNA fragments. The protein is the bright spot located in the middle of the bent DNA fragments. Molecular Cell 2002 9, 187-194DOI: (10.1016/S1097-2765(02)00435-5)

Figure 3 Superposition of Two 12 bp B-DNA Molecules on the Ocr Dimer (A) The view is identical to that in Figure 1C. A least squares fit of phosphate groups of the B-DNA complex (pdb code 1BNA) was made onto 12 carboxyl groups of ocr (see text) giving an rms fit of 1.9 Å (The pairs of amino acid side-chain and phosphate used in the fit are labeled). The phosphorus atoms are colored yellow, and oxygen atoms of the phosphate groups are colored purple. The 12 carboxyl groups are colored red (oxygen) and black (carbon). The sugar backbones of the DNA dimer chains are colored in two shades of green, and the base pairs are omitted for clarity. (B) The view is identical to that in Figure 1B and colored as in (A). The 2-fold axis lies in the plane of the paper. The vectors describing the direction of the fitted DNA (17) on both halves of the dimer are drawn as black lines. Their intersection gives a bend angle of 33.6°. Molecular Cell 2002 9, 187-194DOI: (10.1016/S1097-2765(02)00435-5)