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Figure 2.
Fig. 2. Final 2F[o] − F[c] and omit difference F[o] −
F[c] electron density maps of the nucleotide-binding pocket of
PspF[1–275]. (a) Final 2F[o] − F[c] map of the
Mg-AMP-PspF[1–275] structure at 2.85 Å resolution
contoured at 1σ. The neighbouring subunit is coloured magenta.
Important intramolecular catalytic residues are highlighted and
important intermolecular catalytic residues offered by the
neighbouring subunit are denoted ‘t’ for ‘trans’. Note
how the extra electron density encircled in green dashed lines
occupies the position of the γ phosphate in ATP-bound
structures of PspF[1–275] and is connected to the electron
density of the AMP moiety. (b) Omit difference F[o] − F[c] map
of the Mg-AMP-PspF[1–275] structure contoured at 3σ. The
PspF[1–275]-ATP-bound structure was superimposed onto the P
loop of the PspF[1–275]-Mg-AMP-bound structure and the result
is displayed in this figure. Note that ATP fits convincingly
into the difference map. Further note how the γ phosphate of
ATP fits into the extra density encircled in (a). Data were
collected at ESRF beamline ID-29. Refinement of the structure
was performed as described^14 and the nucleotide and the Mg ion
were refined with unit occupancy. Map inspection, model building
and water molecule picking were done using Coot.^18 The average
temperature factors in this structure are 30 for the protein, 60
for the AMP and 57 for the Mg. For analysis, all the liganded
(ATP: 2C96; ADP: 2C98; AMPPNP: 2C99; Mg-ATP-PspF[1–275]R227A:
2C9C) and unliganded (Apo: 2BJW) PspF structures were aligned
onto their P loops (residues 35 to 43). All figures were
prepared using Pymol (Delano, W. L. (2002). The PyMOL Molecular
Graphics System on the World Wide Web, http://www.pymol.org).
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