Structural constraints of the nucleotide binding site of Gta.
The atomic coordinates for the Gta-GTPgS complex (Noel et al., 1993) obtained
from the Protein Data Bank (Bernstein et al., 1977; Abola et al., 1987)
were used to generate secondary structure representations (white ribbon
diagram) and calculated electron densities, contoured at the van der Waals
radii, for amino acid residues (red cage-like surfaces) that form the binding
site for GTPgS (green), using the program CHAIN (Sack, 1988). Mg2+
is shown in blue. A, Ribbon display showing GTPgS (stick diagram)
binding between the GTPase (1-5 and 1-6) and the -helical (A-G) domains.
B, Close up of the same view as A; showing the F backbone carbonyls
of Leu 171 and Arg 172, (red) accepting hydrogen bonds from the ribose
2' and 3' hydroxyls (green), with the donor and acceptor oxygens labeled
'O'. In this view, the loops forming the H-bonding network to GTPgS
are shown: D-E, F-L2, 5-G, 1-1, 3-""2, & 6-5. C, Same view showing
the electron density for residues (red) that surround GTPgS (green). Non-bridging
g-phosphate oxygens and sulfur are indicated in white. Ribose hydroxyls
are enclosed by residues from F-L2 and D-E loops, and the ( sulfur is enclosed
by L2, 3-""2 loop. Small regions lacking density are on the order
of 5 in diameter. D-F, Views rotated from that of C ("front")
in 90° increments (toward the viewer) about the x-axis; viewed from
the top (D), back (E), and bottom (F). To display internal details
clearly in close-up views, portions of the Gta structure far from the nucleotide
binding site have been clipped.
Abola, E. E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., & Weng,
J.(1987) Protein Data Bank in Crystallographic Databases-Information Content,
Software Systems, Scientific Applications, eds. F.H. Allen, G. Bergerhoff,
and R. Sievers, Data Commission of the International Union of Crystallography,
Bonn/Cambridge/Chester, pp. 107-132.
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr.,
Brice, M.D., Rodgers, J.R., Abola, E. E., Bernstein, F.C., Bryant, S.H.,
Koetzle, T.F., & Weng, J.(1987) Protein Data Bank in Crystallographic
Databases-Information Content, Software Systems, Scientific Applications,
eds. F.H. Allen, G. Bergerhoff, and R. Sievers, Data Commission of the
International Union of Crystallography, Bonn/Cambridge/Chester, pp. 107-132.
Noel, J. P., Hamm, H. E. and Sigler, P. B. (1993) Nature 366,654-663.
Sack, J.S. (1988) J. Mol. Graphics 6 224-225.