1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Trempe, J.-F.
Gehring, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 F N3 O7 P
325.188
n
4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one
2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H13 F N5 O7 P
365.212
n
2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE
2'-FLUORO-2-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 F N2 O8 P
340.199
n
2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'-PHOSPHATE
DNA linking
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
123
4896
4903
10.1021/ja003859p
11457316
NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.
2001
10.2210/pdb1fc8/pdb
pdb_00001fc8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3790.341
5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3'
1
syn
polymer
RNA/2'F-ANA HAIRPIN
no
yes
GGAC(DT)(DT)(DC)(DG)(GFL)(TAF)(CFL)(CFL)
GGACTTCGGTCC
A
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
n
n
n
-4.075
1
19
A
1
A
12
-1.939
A_G1:CFL12_A
1
-4.793
-0.396
0.080
-0.303
1.420
1
19
A
2
A
11
3.196
A_G2:CFL11_A
2
-9.232
-1.075
-0.446
-0.507
10.512
1
20
A
3
A
10
3.408
A_A3:TAF10_A
3
-2.561
-0.051
-0.723
-0.320
14.008
1
19
A
4
A
9
3.096
A_C4:GFL9_A
4
0.533
0.717
-0.343
-0.254
3.595
32.689
A
A
1
2
-3.683
A
A
12
11
3.480
-2.066
0.592
-1.230
AA_G1G2:CFL11CFL12_AA
1
4.064
-7.243
32.379
-1.797
-0.288
2.891
37.824
A
A
2
3
13.456
A
A
11
10
3.147
8.650
0.764
-0.733
AA_G2A3:TAF10CFL11_AA
2
-0.796
1.239
36.849
-2.172
-1.275
3.320
33.636
A
A
3
4
6.339
A
A
10
9
3.546
3.661
0.800
-1.741
AA_A3C4:GFL9TAF10_AA
3
-0.908
1.572
33.430
-3.638
-1.539
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2001-05-30
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2000-07-18
REL
REL
SOLID PHASE SYNTHESIS; PHOSPHORAMIDITE CHEMISTRY
sample
This structure was determined using standard 2D homonuclear techniques.
RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM
5
5
2D NOESY
2D NOESY
DQF-COSY
2D 1H-13C HMQC
2D 1H-31P HETCOR
2D 1H-19F HETCOR
0.066
7.2
ambient
293
K
SA at 15000K for 15 psec from random coordinates.
Refinement from lower energy structure at 3000K fro 9 psec.
5 structures generated.
Total of 305 restraints:
98 intraresidue NOE-derived distance constraints,
94 sequential NOE-derived distance constraints,
3 long range NOE-derived distance constraints,
15 distance restraints from hydrogen bonds,
91 dihedral angle restraints,
4 planarity constraints for base pairs
Distance geometry,
simulated annealing
3
closest to the average
0.5 mM Oligonucleotide hairpin;
90% H2O, 10% D2O
90% H2O/10% D2O
0.5 mM Oligonucleotide hairpin;
D2O
D2O
BRUNGER
structure solution
X-PLOR
3.843
BRUNGER
refinement
X-PLOR
3.843
500
Bruker
DRX
400
Bruker
DMX
750
Varian
UNITYPLUS
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
C
4
n
4
C
4
A
T
5
n
5
DT
5
A
T
6
n
6
DT
6
A
C
7
n
7
DC
7
A
G
8
n
8
DG
8
A
+G
9
n
9
GFL
9
A
+T
10
n
10
TAF
10
A
+C
11
n
11
CFL
11
A
+C
12
n
12
CFL
12
A
author_defined_assembly
1
monomeric
A
GFL
9
A
GFL
9
DG
A
TAF
10
A
TAF
10
DT
A
CFL
11
A
CFL
11
DC
A
CFL
12
A
CFL
12
DC
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
2
A
A
HO2'
O4'
C
DT
4
5
1.56
3
A
A
O2
H22
DT
DG
6
8
1.60
1
4.72
0.50
113.10
117.82
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.71
0.50
113.10
117.81
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
3.68
0.50
113.80
117.48
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.96
0.50
113.10
118.06
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
2
4.68
0.50
113.10
117.78
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
2
-2.46
0.40
106.40
103.94
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
2
4.76
0.50
113.10
117.86
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
2
-2.62
0.40
106.40
103.78
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
2
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
2
2.01
0.30
108.30
110.31
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
2
4.93
0.50
113.10
118.03
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
3
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
3
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
3
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
3
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
3
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
3
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
3
4.88
0.50
113.10
117.98
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
3
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
4
4.70
0.50
113.10
117.80
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
4
-2.54
0.40
106.40
103.86
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
4
4.63
0.50
113.10
117.73
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
4
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
4
3.67
0.50
113.80
117.47
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
4
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
4
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
4
4.83
0.50
113.10
117.93
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
5
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
5
-2.50
0.40
106.40
103.90
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
5
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
5
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
5
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
5
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
C
C
C
4
4
4
N
5
2.01
0.30
108.30
110.31
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
5
3.15
0.30
108.30
111.45
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
5
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)
1
N
N
covale
1.619
both
A
DG
8
A
O3'
DG
8
1_555
A
GFL
9
A
P
GFL
9
1_555
covale
1.623
one
A
GFL
9
A
O3'
GFL
9
1_555
A
TAF
10
A
P
TAF
10
1_555
covale
1.622
one
A
TAF
10
A
O3'
TAF
10
1_555
A
CFL
11
A
P
CFL
11
1_555
covale
1.616
one
A
CFL
11
A
O3'
CFL
11
1_555
A
CFL
12
A
P
CFL
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
CFL
12
A
N3
CFL
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
CFL
12
A
O2
CFL
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
CFL
12
A
N4
CFL
12
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
CFL
11
A
N3
CFL
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
CFL
11
A
O2
CFL
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
CFL
11
A
N4
CFL
11
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
TAF
10
A
N3
TAF
10
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
TAF
10
A
O4
TAF
10
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
GFL
9
A
N1
GFL
9
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
GFL
9
A
O6
GFL
9
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
GFL
9
A
N2
GFL
9
1_555
hydrog
DT-GFL MISPAIR
A
DT
5
A
O2
DT
5
1_555
A
GFL
9
A
N1
GFL
9
1_555
RNA/DNA CHIMERA
2'F-ARABINONUCLEIC ACID, RNA, DNA, HYBRID DUPLEX, HAIRPIN, RNA-DNA CHIMERA COMPLEX
1FC8
PDB
1
1FC8
1
12
1FC8
1
12
1FC8
A
1
1
12
1
P 1