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Figure 3.
Figure 3. Hydrophobic and polar interactions between dT[6]
and Bs-CspB. (a) The contact surface of Bs-CspB is shown as a
semitransparent grey object, protein groups involved in stacking
interactions and hydrogen bonding are colored according to the
CPK scheme with the exception of carbon which is in green.
Hydrogen bonds between protein and DNA groups are depicted as
dotted lines. This is a stereo picture. (b) Representative
section from the continuous arrangement of DNA (black)
interacting with Bs-CspB groups (grey), displayed as
structural formulas (bb, protein backbone). All parts of a
complete binding site from a single protein molecule are
highlighted by a grey box. Stacking interactions between
aromatic side-chains and nucleobases, originating from the
centers (stack) or rims (edge-on stack) of the aromatic rings
are depicted as solid grey lines. Interactions involving
hydrogen bonds are displayed as dotted lines, water molecules
mediating protein–ligand interactions are depicted as small
spheres. Adjacent side-chains belong to symmetry related
molecules. The numbers of the contact subsites for individual
nucleobases are given at the bottom. These subsites are
discussed in the text.
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