Figure 1.
Fig. 1. Electron density for the nucleotide analogs.
Stereodiagrams are shown for the active site contents of the
complexes of the six nanologs with S1dC as follows: a, o-NPhAE;
b, m-NPhAE; c, p-NPhAE; d, o,p-NPhAE; e, o,p-DNPhAP; f,
N-methyl-NPhAE. The nanologs and Mg2+ atoms were removed from
the coordinate file, and the structure was submitted to one
round of least squares refinement with TNT (31). The subsequent
omit map, created with coefficients of the form F[o] F[c], was
contoured at 2.5 and used
to create the figures. The residues that form the P-loop which
wraps around the triphosphate region of the nucleotide,
Ser181-Asn188, are shown as ball and stick. Additionally, the
N-terminal region that forms the binding pocket for the
nucleotide (Asn127-Pro133) is included. The side chains for
Asn127, Phe^129, and Arg131 are represented with ball and stick
atoms. The atoms are colored by atom type for the nanologs as
follows: carbon, gray; oxygen, red; nitrogen, blue; beryllium,
green; fluorine, yellow; phosphorus, magenta; and magnesium,
orange. All protein atoms are colored gray. Figs. 1-4 were
prepared with the programs Molscript and Molded (18, 54).
The above figure is reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
398-408)
copyright 2000.
F[c], was
contoured at 2.5 
and used
to create the figures. The residues that form the P-loop which
wraps around the triphosphate region of the nucleotide,
Ser181-Asn188, are shown as ball and stick. Additionally, the
N-terminal region that forms the binding pocket for the
nucleotide (Asn127-Pro133) is included. The side chains for
Asn127, Phe^129, and Arg131 are represented with ball and stick
atoms. The atoms are colored by atom type for the nanologs as
follows: carbon, gray; oxygen, red; nitrogen, blue; beryllium,
green; fluorine, yellow; phosphorus, magenta; and magnesium,
orange. All protein atoms are colored gray. Figs. 1-4 were
prepared with the programs Molscript and Molded (18, 54).