|
Figure 2.
Figure 2. Nucleotide Binding by D2(A) Stereo view of the
refined 2F[o]−F[c] electron density map within 2.4 Å of
AMPPNP, contoured at 1.5 σ. The refined model is shown with
AMPPNP and Mg^2PLUSPUSSIGN in black, and protein and water
molecules in white. The figure was prepared with BOBSCRIPT
([18]).(B) Stereo view of nucleotide-binding site. AMPPNP is
shown with black bonds. White, light gray, dark gray, and black
spheres denote carbon, nitrogen, oxygen, and phosphorus atoms,
respectively. Mg^2PLUSPUSSIGN is shown as a larger black sphere.
Water molecules are shown as single oxygen atoms. Hydrogen bonds
are shown as thin dashed lines; Mg^2PLUSPUSSIGN coordination
bonds are shown as thick dashed lines. For clarity, the backbone
at position 510 and the water molecule that interacts with the
α-phosphate oxygens (see [C]) are not shown.(C) Schematic
diagram of the interactions between AMPPNP and D2. Water
molecules are indicated by “W.” Hydrogen and Mg^2PLUSPUSSIGN
coordination bonds are indicated with dashed lines. Main-chain
amide and carbonyl oxygen groups that interact with the ligand
are shown emanating from the box surrounding the residue name,
and side chain functionalities are shown schematically. Nonpolar
van der Waals contacts are indicated by arcs. In (B) and (C),
the asterisk at Lys-639 designates that this residue comes from
an adjacent protomer in the D2 hexamer. This lysine appears to
be only partially occupied, and its interaction with Oγ of
AMPPNP is likely replaced by a water molecule in a fraction of
the molecules in the crystal (see text).
|
