Figure 1.
Fig 1. Divalent cation binding sites on nucleosomal DNA.
(A) Location of the Mn2+ binding sites in one half of the DNA
superhelix (79 of 147 bp, 0 indicates the central base pair and
5' and 3' labels indicate the DNA terminus). All filled sites (
)
occur at GG or GC base pair steps in the DNA major groove except
for one site in the minor groove. The site numbers, including
vacant GG and GC base pair steps (x), correspond to Table 1. DNA
bases are shaded according to whether the major (gray) or minor
(white) groove faces inward. The DNA backbone is colored
according to the value of the base pair-step roll parameter as
indicated (Roll). (B and C) Electron density for Mn2+ sites 1-GG
and 5-GC, respectively. Anomalous difference electron density
(green, 4 contour) denotes the
location of the Mn2+ ions, and simulated annealing, omit
difference electron density (yellow, F[o] - F[c] 1.5 and 2
contours, respectively)
corresponds to the positions of the metal-coordinated water
molecules (five first shell, one second shell). Coordination
bonds (magenta) between metal ion (magenta) and water molecules
(red) are shown in the context of the surrounding base pair
steps.
)
occur at GG or GC base pair steps in the DNA major groove except
for one site in the minor groove. The site numbers, including
vacant GG and GC base pair steps (x), correspond to Table 1. DNA
bases are shaded according to whether the major (gray) or minor
(white) groove faces inward. The DNA backbone is colored
according to the value of the base pair-step roll parameter as
indicated (Roll). (B and C) Electron density for Mn2+ sites 1-GG
and 5-GC, respectively. Anomalous difference electron density
(green, 4 
contour) denotes the
location of the Mn2+ ions, and simulated annealing, omit
difference electron density (yellow, F[o] - F[c] 1.5