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PDBsum entry 1em0
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PDB id:
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DNA
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Title:
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Complex of d(cctagg) with tetra-[n-methyl-pyridyl] porphyrin
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Structure:
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DNA (5'-d( (Cbr)p Cp Tp Ap Gp G)-3'). Chain: a, b, c, d. Engineered: yes
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Source:
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Synthetic: yes
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Resolution:
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0.90Å
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R-factor:
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0.151
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R-free:
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0.172
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Authors:
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S.Neidle,M.Sanderson,M.Bennett,A.Krah,F.Wien,E.Garman,R.Mckenna
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Key ref:
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M.Bennett
et al.
(2000).
A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling.
Proc Natl Acad Sci U S A,
97,
9476-9481.
PubMed id:
DOI:
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Date:
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14-Mar-00
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Release date:
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21-Aug-00
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Headers
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References
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CBR-C-T-A-G-G
6 bases
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CBR-C-T-A-G-G
6 bases
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CBR-C-T-A-G-G
6 bases
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CBR-C-T-A-G-G
6 bases
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DOI no:
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Proc Natl Acad Sci U S A
97:9476-9481
(2000)
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PubMed id:
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A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling.
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M.Bennett,
A.Krah,
F.Wien,
E.Garman,
R.McKenna,
M.Sanderson,
S.Neidle.
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ABSTRACT
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The crystal structure of a B-type DNA hexanucleotide duplex complexed with the
porphyrin has been solved by
multiwavelength anomalous diffraction phasing and refined to an R factor of
11.5% at a resolution of 0.9 A. The structure has been solved and refined as two
crystallographically independent duplexes, stacked end to end. Contrary to
expectation, the porphyrin molecule is not intercalated into the duplex but is
stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly
buckled as a consequence of the nickel coordination, which produces large
changes in local DNA structure. A second mode of porphyrin binding is apparent
as a consequence of crystal packing, which places the ligand in the minor groove
of an adjacent duplex. This structure thus provides, to our knowledge, the first
atomic visualization of minor-groove binding for a porphyrin molecule. The
geometry of groove binding provides a ready explanation for porphyrin-induced
DNA strand cleavage at deoxyribose residues.
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Selected figure(s)
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Figure 1.
Fig. 1. (a) The structure of the Ni2+-TMPy ligand. (b)
Final 2F[o]  F[c]
electron density map, calculated in the plane of the Ni2+-TMPy
ligand. (c) plot of the 2:2 complex in the crystallographic
asymmetric unit.
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Figure 4.
Fig. 4. View of the end of one hexamer duplex with bases
shown as idealized polygons and the end-capping Ni2+-TMPy ligand.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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B.M.Zeglis,
V.C.Pierre,
J.T.Kaiser,
and
J.K.Barton
(2009).
A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode.
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Biochemistry,
48,
4247-4253.
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PDB codes:
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O.Ryazanova,
I.Voloshin,
I.Dubey,
L.Dubey,
and
V.Zozulya
(2008).
Fluorescent studies on cooperative binding of cationic pheophorbide-a derivative to polyphosphate.
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Ann N Y Acad Sci,
1130,
293-299.
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K.Wang,
Z.Zhang,
L.Wu,
and
Z.Y.Li
(2007).
Synthesis, and DNA-binding and DNA-photocleavage properties of multiply charged porphyrins.
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Chem Biodivers,
4,
514-522.
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D.H.Tjahjono,
R.E.Kartasasmita,
A.Nawawi,
S.Mima,
T.Akutsu,
N.Yoshioka,
and
H.Inoue
(2006).
Binding of tetrakis(pyrazoliumyl)porphyrin and its copper(II) and zinc(II) complexes to poly(dG-dC)2 and poly(dA-dT)2.
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J Biol Inorg Chem,
11,
527-538.
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Y.Nitta,
and
R.Kuroda
(2006).
Quantitative analysis of DNA-porphyrin interactions.
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Biopolymers,
81,
376-391.
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A.T.Phan,
V.Kuryavyi,
H.Y.Gaw,
and
D.J.Patel
(2005).
Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.
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Nat Chem Biol,
1,
167-173.
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PDB codes:
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P.J.Perry,
J.R.Arnold,
and
T.C.Jenkins
(2001).
Telomerase inhibitors for the treatment of cancer: the current perspective.
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Expert Opin Investig Drugs,
10,
2141-2156.
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S.Neidle,
and
M.A.Read
(2000).
G-quadruplexes as therapeutic targets.
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Biopolymers,
56,
195-208.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
