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Figure 1.
Fig. 1. Fork-junction DNA and electron density map. (A)
Synthetic DNA oligonucleotides used for complex formation and
crystallization. The numbers above denote the DNA position with
respect to the transcription start site at +1. Downstream
corresponds to the direction of RNAP movement during
transcription. Mutations in the bottom DNA strand cause
corresponding mutations in the RNA transcript, defining it as
the template (versus the nontemplate) strand. The DNA sequence
is derived from the full con promoter (4), with -35 and -10
elements (shaded yellow and labeled) as well as an extended -10
element (shaded red and labeled). (B) Stereo view of the Taq
RNAP holoenzyme/fork-junction DNA complex. The  -carbon
backbone of  is
colored white,  cyan, ' pink, and
 orange
(the subunits
are not visible). The DNA template strand is colored dark green,
and the nontemplate strand is light green, except for the -35
and -10 elements, which are colored yellow. The visible
structural domains of ( [2] and
[4]) (1,
9) are labeled. The direction of transcription (downstream) is
to the right. The experimental electron density map, calculated
using observed amplitude (F[o]) coefficients, is shown (blue
net, contoured at 1.5 ), and was
computed using multiple isomorphous replacement phases (Table
1), followed by density modification. The view is sliced at a
level just in front of the DNA to reveal the '
NH[2]-terminal Zn2+-binding domain and the associated Zn2+
(labeled, shown as a green sphere). Shown in red is a difference
Fourier map, calculated using (|F[o]EMTS - F[o]native|)
coefficients (Table 1), revealing the Hg-binding site that was
used to locate the Zn2+-site.
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