Figure 3.
Figure 3: Stereo pairs showing active site stereochemistry in
alternative ligand complexes of AlkB- Delta-N11.
Ligands and side chains are coloured according to atomic
identity as in Fig. 1. a, The anaerobic Michaelis complex has
all of the octahedral coordination sites on the Fe cofactor
occupied by protein or 2OG atoms except for a single site
occupied by a crystallographic water, which must be replaced by
O[2] to initiate oxidation (Supplementary Fig. S1). b,
Equivalent view of the structure co-crystallized with Fe,
succinate and dT-(1-me-dA)-dT (Supplementary Table S2). c,
Equivalent view of the structure in which the anaerobic
Michaelis complex was exposed to oxygen for 2 h. Unbiased
electron density maps (Supplementary Fig. S5B) and occupancy
refinement (Supplementary Table S3) both support the conclusion
that most of the 2OG has been oxidized to succinate but that the
adenine base remains largely methylated after short-term in situ
oxidation. The alternative ligands are shown in semi-transparent
rendering with the degree of transparency scaled according to
refined occupancy. d, Refined 2F[o] - F[c] (green) and F[o] -
F[c] (red) electron density maps for the structure shown in c
contoured at +1 and
-3 ,
respectively. There are no F[o] - F[c] peaks +
3 in
this region.
The above figure is reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2006,
439,
879-884)
copyright 2006.
N11.
Ligands and side chains are coloured according to atomic
identity as in Fig. 1. a, The anaerobic Michaelis complex has
all of the octahedral coordination sites on the Fe cofactor
occupied by protein or 2OG atoms except for a single site
occupied by a crystallographic water, which must be replaced by
O[2] to initiate oxidation (Supplementary Fig. S1). b,
Equivalent view of the structure co-crystallized with Fe,
succinate and dT-(1-me-dA)-dT (Supplementary Table S2). c,
Equivalent view of the structure in which the anaerobic
Michaelis complex was exposed to oxygen for 2 h. Unbiased
electron density maps (Supplementary Fig. S5B) and occupancy
refinement (Supplementary Table S3) both support the conclusion
that most of the 2OG has been oxidized to succinate but that the
adenine base remains largely methylated after short-term in situ
oxidation. The alternative ligands are shown in semi-transparent
rendering with the degree of transparency scaled according to
refined occupancy. d, Refined 2F[o] - F[c] (green) and F[o] -
F[c] (red) electron density maps for the structure shown in c
contoured at +1 
and
-3 
+
3