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![[Figure 3]](lp5065fig3mag.jpg)
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Figure 3
The MD–MX procedure guides remodeling of Lys217 and reveals a bound inorganic phosphate. (a) Coordinates, 2Fo − Fc density (blue, 1σ isosurface) and Fo − Fc density (positive in green and negative in red, 3σ isosurface) from S. (b) Coordinates from Mall, with MD protein (purple, 1σ isosurface), solvent (blue, 3σ isosurface) and chloride density (yellow, 10σ isosurface), from the 90–100 ns segment of the simulation; the MD simulation suggests a different conformation for the side chain and a number of ordered waters; it also includes a spot of chloride density in the same position as the positive difference density in (a). (c) Coordinates, 2Fo − Fc density (blue, 1σ isosurface) and Fo − Fc density (positive in green and negative in red, 3σ isosurface) from Ri; the shape of the difference density is suggestive of a coordinated free phosphate molecule. (d) Coordinates, 2Fo − Fc density (blue, 1σ isosurface) and Fo − Fc density (positive in green and negative in red, 3σ isosurface) from model Rf refined against the high-resolution data (PDB entry 7v0g): the revised side-chain conformation, water network and phosphate are plausible and improve the difference density in the region. His158 is also shown as a reference point. Polder OMIT map density for the phosphate is shown at a level of 5σ (orange) confirming that the addition of this molecule is reasonable. |
![[Figure 3]](lp5065fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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