Volume 8, Issue 4, Pages 441-452 (April 2000) A high-resolution structure of a DNA–chromomycin–Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance  Miriam Gochin  Structure  Volume 8, Issue 4, Pages 441-452 (April 2000) DOI: 10.1016/S0969-2126(00)00124-6

Figure 1 The chromomycin chemical structure showing the residue numbering. Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)

Figure 2 13C–1H heteronuclear multiple quantum coherence spectra of d(TTGGCCAA)2 complexed with chromomycin and cobalt (left) or zinc (right). Spectra were recorded at 500 MHz and 25°C. Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)

Figure 3 (a) View into the minor groove of 1d83 and (b) the minimized average structure obtained from pseudocontact shift+NOE refinement. The DNA is represented as a molecular surface, with bases and the backbone shown in green and magenta, respectively, for (a) 1d83, and in cyan and red, respectively, for (b) the shift-based structure. Chromomycin is shown as a stick figure bound in the minor groove, and is orange in 1d83 and yellow in the shift-based structure. Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)

Figure 4 The central four base pairs G3–C6, G13–C16 of the DNA in the complex with chromomycin-A3 and divalent metal in (a) the original published PDB structure 1d83 and (b) the new shift-based structure. Backbone atoms are shown in light grey and bases in dark grey. Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)

Figure 5 DNA helix axis representation for the DNA in the complex with chromomycin-A3 and divalent metal in the original PDB structure of (a) d(AAGGCCTT)2 and (b) the shift-based structure of d(TTGGCCAA)2. Axes were calculated using Curves 5.1 [17]. Also indicated is the distance between penultimate base pairs of each DNA segment. Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)

Figure 6 Detailed regions of the structure of the DNA with chromomycin-A3. (a) A segment G13–G14–C15 of DNA and parts of the chromophore residue chr23, as well as A sugar A22 and E sugar E34 of the drug, drawn to illustrate the steric interaction of methyl groups on the drug. On the left is 1d83 in magenta (DNA backbone), green (bases) and orange (drug) and on the right is the shift-based structure in red (DNA backbone), cyan (bases) and yellow (drug). (b) Hydrogen-bonding network between the C36, D35, E34 trisaccharide segment of one drug molecule and the A22 sugar of the second, as well as to the non-hydrogen-bonded amino protons on G13 and G14. Only exchangeable protons involved in hydrogen bonds appear explicitly. Protons shown in yellow are slowly exchanging in the NMR. Carbon atoms shown in green have attached protons that exhibit NOEs to D-HO4 in Figure 7. All other atoms are color coded in grey (carbon, phosphorus), red (oxygen), blue (nitrogen) and white (hydrogen). On the left is the hydrogen-bonding in 1d83, and on the right in the shift-based structure (see text). Hydrogen bonds are drawn for distances of less than 2.5 Å. (c) Superposition of three shift+NOE based minimized average structures (see text) at the chromophore ring atoms of chr33, in order to demonstrate sidechain orientations consistent with all data. Possible hydrogen bonds between chromophore sidechain HO4′ and a phosphate oxygen at the C5–C6 step, and between the sidechain HO3′ (one structure only) and a phosphate oxygen at the C6–A7 step are shown. Atoms are color coded as in (b). Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)

Figure 7 Portion of the NOESY spectrum of a 2 mM sample of d(TTGGCCAA)2 with chromomycin-A3 and Co2+ in 90% H2O, 10% D2O, showing NOE connectivities between the slowly exchanging HO4 proton on the D-sugar and protons on the A, D and E sugars. Structure 2000 8, 441-452DOI: (10.1016/S0969-2126(00)00124-6)