 |
PDBsum entry 117d
 |
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Nucleic Acids Res
20:6637-6647
(1992)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG).
|
|
C.Bingman,
S.Jain,
G.Zon,
M.Sundaralingam.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has
been determined to a resolution of 2.55A using oscillation film data. The
crystals belong to space group P6(1) 22, a = b = 46.2A, c = 71.5A with one
strand in the asymmetric unit, and are isomorphous with a previously described
non-alternating dodecamer, d(CCGTACGTACGG) (5'-CC). Refinement by X-PLOR/NUCLSQ
gave a final R factor of 14.2% for 1089 observations. The molecule adopts the
A-DNA form. The interchange of the terminal base pairs in the two dodecamers
results in differences in the intermolecular contacts and may account for the
differences in the bending. This dodecamer shows an axial deflection of 30
degrees, in the direction of the major groove compared to 20 degrees in 5'-CC
and may be a consequence of additional contacts generated in 5'-GC by the
interchange of end base pairs. The high helical axis deflection appreciably
influences the local helical parameters. The molecule exhibits relatively high
inclination angles, and has a narrow major groove. The helical parameters when
described relative to the dyad-related hexamer halves of the molecule give more
reasonable values. The crystal packing, local helical parameters, torsion
angles, and hydration are described and also compared with the non-alternating
5'-CC dodecamer.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
T.A.Soares,
P.H.Hünenberger,
M.A.Kastenholz,
V.Kräutler,
T.Lenz,
R.D.Lins,
C.Oostenbrink,
and
W.F.van Gunsteren
(2005).
An improved nucleic acid parameter set for the GROMOS force field.
|
| |
J Comput Chem,
26,
725-737.
|
|
|
|
|
|
|
D.Jose,
and
D.Porschke
(2004).
Dynamics of the B-A transition of DNA double helices.
|
| |
Nucleic Acids Res,
32,
2251-2258.
|
|
|
|
|
|
|
X.Shui,
L.McFail-Isom,
G.G.Hu,
and
L.D.Williams
(1998).
The B-DNA dodecamer at high resolution reveals a spine of water on sodium.
|
| |
Biochemistry,
37,
8341-8355.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Pan,
C.Ban,
M.C.Wahl,
and
M.Sundaralingam
(1997).
Crystal structure of d(GCGCGCG) with 5'-overhang G residues.
|
| |
Biophys J,
73,
1553-1561.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Hartmann,
and
R.Lavery
(1996).
DNA structural forms.
|
| |
Q Rev Biophys,
29,
309-368.
|
|
|
|
|
|
|
C.Ban,
B.Ramakrishnan,
and
M.Sundaralingam
(1996).
Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I.
|
| |
Biophys J,
71,
1215-1221.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.Guzikevich-Guerstein,
and
Z.Shakked
(1996).
A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein.
|
| |
Nat Struct Biol,
3,
32-37.
|
|
|
|
|
|
|
M.A.Young,
G.Ravishanker,
D.L.Beveridge,
and
H.M.Berman
(1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
|
| |
Biophys J,
68,
2454-2468.
|
|
|
|
|
|
|
M.Suzuki,
and
N.Yagi
(1995).
Stereochemical basis of DNA bending by transcription factors.
|
| |
Nucleic Acids Res,
23,
2083-2091.
|
|
|
|
|
|
|
X.Chen,
B.Ramakrishnan,
S.T.Rao,
and
M.Sundaralingam
(1994).
Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.
|
| |
Nat Struct Biol,
1,
169-175.
|
|
|
PDB code:
|
|
|
|
|
|
|
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
code is
shown on the right.
|
|
Links
