Figure 2.
FIGURE 2. The DNA binding region in RuvBL1 domain II. A,
stereoview of the protein C^ trace (gold) and ssDNA
ball-and-stick representation (carbon, nitrogen, oxygen, and
phosphorus atoms are colored gray, blue, red, and green,
respectively) of the RPA molecule (PDB 1JMC) superimposed onto
the DNA binding region of RuvBL1 DII (residues 127-233; cyan).
The long loops in the N-terminal domain of RPA that interact
with ssDNA (arrows 1 and 3) correspond to a disordered loop and
a much shorter loop (arrow 2) in RuvBL1 DII. B, view of the
electrostatic potential of the RPA molecule mapped at its
molecular surface. The molecular surface was calculated with
MSMS (65) using a probe radius of 1.4 Å, and the
electrostatic potential was calculated with MEAD (66) using an
ionic strength of 0.1 M, dielectric constants of 4.0 and 80.0
for the protein and the exterior, respectively, and a
temperature of 300 K. The range of potentials shown spans -5
(red) to +5 kT/e (blue) units. C, view of the electrostatic
potential of the DNA binding region of RuvBL1 DII mapped at its
molecular surface. The molecular surface and the electrostatic
potential were calculated as described above for the whole
RuvBL1 hexamer, but for clarity only the DNA binding region of
RuvBL1 DII is represented. As a visual aid, the ssDNA molecule
bound to RPA is represented in ball-and-stick (Carbon, nitrogen,
oxygen, and phosphorus atoms are colored gray, blue, red, and
green, respectively). The view in B and C is the same as in Fig.
2A. Drawings were prepared with DINO.
trace (gold) and ssDNA
ball-and-stick representation (carbon, nitrogen, oxygen, and
phosphorus atoms are colored gray, blue, red, and green,
respectively) of the RPA molecule (PDB 1JMC) superimposed onto
the DNA binding region of RuvBL1 DII (residues 127-233; cyan).
The long loops in the N-terminal domain of RPA that interact
with ssDNA (arrows 1 and 3) correspond to a disordered loop and
a much shorter loop (arrow 2) in RuvBL1 DII. B, view of the
electrostatic potential of the RPA molecule mapped at its
molecular surface. The molecular surface was calculated with
MSMS (65) using a probe radius of 1.4 Å, and the
electrostatic potential was calculated with MEAD (66) using an
ionic strength of 0.1 M, dielectric constants of 4.0 and 80.0
for the protein and the exterior, respectively, and a
temperature of 300 K. The range of potentials shown spans -5
(red) to +5 kT/e (blue) units. C, view of the electrostatic
potential of the DNA binding region of RuvBL1 DII mapped at its
molecular surface. The molecular surface and the electrostatic
potential were calculated as described above for the whole
RuvBL1 hexamer, but for clarity only the DNA binding region of
RuvBL1 DII is represented. As a visual aid, the ssDNA molecule
bound to RPA is represented in ball-and-stick (Carbon, nitrogen,
oxygen, and phosphorus atoms are colored gray, blue, red, and
green, respectively). The view in B and C is the same as in Fig.
2A. Drawings were prepared with DINO.