Figure 3.
Fig. 3. SRP54 NG domain–RNA interactions. (A) The
molecular surface of the SRP54 NG domain (Left) and 7S.S RNA
(Right) are shaded to indicate the different accessibilities of
the surface areas at each residue (Left) and nucleotide (Right)
between the free and complexed forms. The red areas define
protein–RNA contacts. The molecule to the right is rotated by
180° with respect to the molecule to the left. (B)
Interaction between the G domain loop connecting G1 and
G2
and the RNA minor groove of helix 5. The side chains of Arg-122
and Lys-126 bind to the phosphate oxygen of A186 and the 2'-OH
atom of C187 in the RNA strand that switches from helix 6 to 8.
The main-chain oxygen of Lys-126 is hydrogen-bonded to the 2'-OH
of C188, and forms a water-mediated contact with the guanine
base of G231, the base partner of C187 in the G–C pair
immediately above the three-way junction. Furthermore, the side
chain of Lys-130 interacts with the phosphate group of C233. RNA
is colored in red, protein residues are colored in blue, and
hydrogen bonds are colored in green.
G1 and
G2
and the RNA minor groove of helix 5. The side chains of Arg-122
and Lys-126 bind to the phosphate oxygen of A186 and the 2'-OH
atom of C187 in the RNA strand that switches from helix 6 to 8.
The main-chain oxygen of Lys-126 is hydrogen-bonded to the 2'-OH
of C188, and forms a water-mediated contact with the guanine
base of G231, the base partner of C187 in the G–C pair
immediately above the three-way junction. Furthermore, the side
chain of Lys-130 interacts with the phosphate group of C233. RNA
is colored in red, protein residues are colored in blue, and
hydrogen bonds are colored in green.