1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Ghosh, M.
Rumpal, N.
Varshney, U.
Chary, K.V.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-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
C9 H13 N2 O8 P
308.182
y
2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
269
1886
1894
10.1046/j.1432-1033.2002.02837.x
11952790
Structural basis for poor uracil excision from hairpin DNA. An NMR study.
2002
10.2210/pdb1idx/pdb
pdb_00001idx
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
Uracil containing hairpin DNA
5483.537
5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*UP*TP*GP*GP*AP*TP*CP*CP*T)-3'
1
syn
polymer
no
no
(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DT)(DU)(DT)(DG)(DG)(DA)(DT)(DC)(DC)(DT)
AGGATCCTTUTGGATCCT
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-8.992
1
20
A
1
B
A
9
0.917
A_DA1:DT9B_A
1
-16.415
0.024
-0.201
-0.100
-1.732
1
19
A
2
B
A
8
-0.526
A_DG2:DC8B_A
2
-1.320
-0.394
0.091
-0.172
5.799
1
19
A
3
B
A
7
-0.556
A_DG3:DC7B_A
3
-6.145
-0.471
0.074
-0.197
-3.990
1
20
A
4
B
A
6
4.570
A_DA4:DT6B_A
4
-15.668
-0.035
-0.218
-0.110
-0.735
1
20
A
5
B
A
5
-1.155
A_DT5:DA5B_A
5
-11.333
0.034
-0.249
-0.124
7.208
1
19
A
6
B
A
4
0.711
A_DC6:DG4B_A
6
3.385
0.419
0.189
-0.180
26.964
1
19
A
7
B
A
3
0.553
A_DC7:DG3B_A
7
-4.107
0.558
-0.808
-0.185
24.964
1
16
A
8
B
A
2
-3.111
A_DT8:DT2B_A
8
53.017
-2.457
-0.750
-1.989
2.451
30.022
A
A
1
2
11.123
B
B
A
A
9
8
2.896
5.725
-0.004
-2.088
AA_DA1DG2:DC8BDT9B_AA
1
-1.728
3.358
29.434
-5.003
-0.286
2.385
31.678
A
A
2
3
14.765
B
B
A
A
8
7
2.894
7.976
0.687
-1.782
AA_DG2DG3:DC7BDC8B_AA
2
0.888
-1.644
30.670
-4.472
-1.124
2.367
32.916
A
A
3
4
22.485
B
B
A
A
7
6
3.301
12.429
0.421
-1.961
AA_DG3DA4:DT6BDC7B_AA
3
2.416
-4.370
30.446
-5.374
-0.371
2.959
26.479
A
A
4
5
4.704
B
B
A
A
6
5
3.128
2.152
-0.613
-1.801
AA_DA4DT5:DA5BDT6B_AA
4
0.623
-1.363
26.386
-4.464
1.492
2.333
30.071
A
A
5
6
15.829
B
B
A
A
5
4
3.022
8.062
-0.084
-2.055
AA_DT5DC6:DG4BDA5B_AA
5
-5.974
11.729
28.384
-5.354
-0.870
2.046
28.280
A
A
6
7
13.650
B
B
A
A
4
3
2.685
6.587
-0.444
-2.087
AA_DC6DC7:DG3BDG4B_AA
6
4.074
-8.441
27.220
-5.398
1.605
1.494
22.106
A
A
7
8
-0.052
B
B
A
A
3
2
4.714
-0.014
-0.638
-4.133
AA_DC7DT8:DT2BDG3B_AA
7
-21.740
79.624
4.030
-10.770
-11.786
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-05-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study
Solution structure of a uracil containing hairpin DNA.
Structural basis for Uracil DNA Glycosylase interaction with Uracil: NMR study
Structural basis for Uracil DNA Glycosylase interaction with Uracil: NMR study
RCSB
Y
RCSB
2001-04-05
REL
Custom made by Ransom Hill Biosciences, Inc., Ramona CA (USA)
sample
This structure was determined using 2D homonuclear techniques
structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
200
6
2D NOESY
E-COSY
2D NOESY
7.0
1
atm
305
K
7.0
1
atm
295
K
The structures are based on a total of 196 restraints, 122 are NOE-derived distance constraints, 64 dihedral angle restraints, 10 distance restraints from hydrogen bonds.
Restrained molecular dynamics and Energy minimization
1
fewest violations,lowest energy
2 mM oligo; no buffer; pH = 7.0; 305K; 99% D2O
99% D2O
2 mM oligo; no buffer; pH = 7.0; 305K; 90% H2O + 10% D2O
90% H2O/10% D2O
varian
collection
VNMR
6.1
MSI
structure solution
Discover
97
varian
data analysis
VNMR
6.1
Bruker
collection
UXNMR
3.0
MSI
processing
Felix
97
MSI
data analysis
Felix
97
MSI
refinement
Discover
97
600
Varian
UNITYPLUS
500
Bruker
AMX
A
1
n
1
DA
1
A
G
2
n
2
DG
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
T
5
n
5
DT
5
A
C
6
n
6
DC
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
T
9
n
9
DT
9
A
U
1
n
10
B
DU
1
A
T
2
n
11
B
DT
2
A
G
3
n
12
B
DG
3
A
G
4
n
13
B
DG
4
A
A
5
n
14
B
DA
5
A
T
6
n
15
B
DT
6
A
C
7
n
16
B
DC
7
A
C
8
n
17
B
DC
8
A
T
9
n
18
B
DT
9
A
author_defined_assembly
1
monomeric
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
1
A
DG
2
0.082
SIDE CHAIN
1
A
DT
8
0.094
SIDE CHAIN
1
A
DT
9
0.420
SIDE CHAIN
B
1
A
DT
2
0.073
SIDE CHAIN
B
1
A
DG
3
0.062
SIDE CHAIN
2
A
DG
2
0.071
SIDE CHAIN
2
A
DT
8
0.086
SIDE CHAIN
2
A
DT
9
0.400
SIDE CHAIN
B
2
A
DT
2
0.153
SIDE CHAIN
B
2
A
DG
3
0.058
SIDE CHAIN
3
A
DA
1
0.061
SIDE CHAIN
3
A
DG
2
0.064
SIDE CHAIN
3
A
DT
8
0.080
SIDE CHAIN
3
A
DT
9
0.426
SIDE CHAIN
B
3
A
DT
2
0.065
SIDE CHAIN
4
A
DG
2
0.076
SIDE CHAIN
4
A
DT
8
0.090
SIDE CHAIN
4
A
DT
9
0.406
SIDE CHAIN
B
4
A
DT
2
0.076
SIDE CHAIN
B
4
A
DG
3
0.065
SIDE CHAIN
B
4
A
DT
6
0.081
SIDE CHAIN
5
A
DG
2
0.082
SIDE CHAIN
5
A
DT
8
0.094
SIDE CHAIN
5
A
DT
9
0.420
SIDE CHAIN
B
5
A
DT
2
0.073
SIDE CHAIN
B
5
A
DG
3
0.062
SIDE CHAIN
6
A
DG
2
0.071
SIDE CHAIN
6
A
DT
8
0.086
SIDE CHAIN
6
A
DT
9
0.400
SIDE CHAIN
B
6
A
DT
2
0.153
SIDE CHAIN
B
6
A
DG
3
0.058
SIDE CHAIN
1
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
-3.20
0.50
117.00
113.80
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
1
3.54
0.50
117.70
121.24
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
1
-3.99
0.60
118.60
114.61
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
1
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
-3.29
0.50
117.00
113.71
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
1
3.40
0.50
117.70
121.10
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
1
-4.78
0.60
118.60
113.82
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
-3.79
0.60
122.90
119.11
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
4.64
0.30
108.30
112.94
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
1.88
0.30
108.30
110.18
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
-5.35
0.80
105.90
100.55
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
1
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-4.84
0.60
122.30
117.46
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
1
-4.57
0.60
122.90
118.33
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
-5.29
0.50
121.30
116.01
A
A
A
C6
N1
C2
DT
DT
DT
9
9
9
N
1
-3.75
0.60
127.20
123.45
A
A
A
C2
N3
C4
DT
DT
DT
9
9
9
N
1
-5.36
0.60
123.70
118.34
A
A
A
C5
C6
N1
DT
DT
DT
9
9
9
N
1
10.64
1.50
120.40
131.04
A
A
A
C6
N1
C1'
DT
DT
DT
9
9
9
N
B
B
B
1
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DU
DU
DU
1
1
1
N
B
B
B
1
5.68
0.60
114.90
120.58
A
A
A
N1
C2
N3
DU
DU
DU
1
1
1
N
B
B
B
1
-5.98
0.70
122.20
116.22
A
A
A
N3
C2
O2
DU
DU
DU
1
1
1
N
B
B
B
1
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
B
B
B
1
-4.56
0.60
122.30
117.74
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
B
B
B
1
-4.32
0.60
122.90
118.58
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
B
B
B
1
-4.95
0.80
105.90
100.95
A
A
A
O4'
C1'
C2'
DG
DG
DG
3
3
3
N
B
B
B
1
6.71
0.30
108.30
115.01
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
B
B
B
1
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
B
B
B
1
-5.06
0.80
105.90
100.84
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
B
B
B
1
3.84
0.50
117.70
121.54
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
B
B
B
1
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
B
B
B
1
-3.95
0.60
122.30
118.35
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
B
B
B
1
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
B
B
B
1
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
B
B
B
1
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
B
B
B
1
-3.65
0.60
122.30
118.65
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
B
B
B
1
-3.89
0.60
122.90
119.01
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
2
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
2
-3.14
0.50
117.00
113.86
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
2
3.46
0.50
117.70
121.16
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
2
-4.10
0.60
118.60
114.50
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
2
-4.82
0.80
105.90
101.08
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
2
4.31
0.30
108.30
112.61
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
2
3.04
0.50
111.50
114.54
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
2
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
2
-3.16
0.50
117.00
113.84
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
2
3.73
0.50
117.70
121.43
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
2
-3.94
0.60
118.60
114.66
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
2
-4.09
0.60
122.30
118.21
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
2
-3.80
0.60
122.90
119.10
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
2
-5.45
0.80
105.90
100.45
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
2
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
2
-4.70
0.60
122.30
117.60
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
2
-4.52
0.60
122.90
118.38
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
2
-5.18
0.50
121.30
116.12
A
A
A
C6
N1
C2
DT
DT
DT
9
9
9
N
2
-5.16
0.60
123.70
118.54
A
A
A
C5
C6
N1
DT
DT
DT
9
9
9
N
2
-3.62
0.60
122.30
118.68
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
2
10.51
1.50
120.40
130.91
A
A
A
C6
N1
C1'
DT
DT
DT
9
9
9
N
B
B
B
2
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N1
DU
DU
DU
1
1
1
N
B
B
B
2
5.86
0.60
114.90
120.76
A
A
A
N1
C2
N3
DU
DU
DU
1
1
1
N
B
B
B
2
-6.34
0.70
122.20
115.86
A
A
A
N3
C2
O2
DU
DU
DU
1
1
1
N
B
B
B
2
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
B
B
B
2
-4.10
0.60
122.30
118.20
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
B
B
B
2
-3.89
0.60
122.90
119.01
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
B
B
B
2
7.02
0.30
108.30
115.32
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
B
B
B
2
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
B
B
B
2
-5.25
0.80
105.90
100.65
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
B
B
B
2
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
B
B
B
2
3.86
0.50
117.70
121.56
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
B
B
B
2
-4.30
0.60
122.30
118.00
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
B
B
B
2
-3.84
0.60
122.90
119.06
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
B
B
B
2
4.30
0.30
108.30
112.60
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
B
B
B
2
-3.76
0.60
122.30
118.54
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
B
B
B
2
-3.95
0.60
122.90
118.95
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
3
-5.40
0.80
105.90
100.50
A
A
A
O4'
C1'
C2'
DA
DA
DA
1
1
1
N
3
6.28
0.30
108.30
114.58
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
3
-3.45
0.50
117.00
113.55
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
3
3.42
0.50
117.70
121.12
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
3
-5.52
0.60
118.60
113.08
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
3
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
3
3.03
0.50
111.50
114.53
A
A
A
C5
C6
N1
DG
DG
DG
3
3
3
N
3
-3.13
0.50
117.00
113.87
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
3
3.52
0.50
117.70
121.22
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
3
-4.41
0.60
118.60
114.19
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
3
-3.80
0.60
122.30
118.50
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
3
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
3
3.73
0.30
108.30
112.03
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
3
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
-5.89
0.80
105.90
100.01
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
3
3.74
0.30
108.30
112.04
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
3
-4.87
0.60
122.30
117.43
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
3
-4.29
0.60
122.90
118.61
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
3
-5.04
0.50
121.30
116.26
A
A
A
C6
N1
C2
DT
DT
DT
9
9
9
N
3
-3.70
0.60
127.20
123.50
A
A
A
C2
N3
C4
DT
DT
DT
9
9
9
N
3
-5.44
0.60
123.70
118.26
A
A
A
C5
C6
N1
DT
DT
DT
9
9
9
N
3
10.07
1.50
120.40
130.47
A
A
A
C6
N1
C1'
DT
DT
DT
9
9
9
N
B
B
B
3
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DU
DU
DU
1
1
1
N
B
B
B
3
5.65
0.60
114.90
120.55
A
A
A
N1
C2
N3
DU
DU
DU
1
1
1
N
B
B
B
3
-5.97
0.70
122.20
116.23
A
A
A
N3
C2
O2
DU
DU
DU
1
1
1
N
B
B
B
3
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
B
B
B
3
-4.40
0.60
122.30
117.90
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
B
B
B
3
-4.28
0.60
122.90
118.62
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
B
B
B
3
7.46
0.30
108.30
115.76
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
B
B
B
3
4.59
0.30
108.30
112.89
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
B
B
B
3
3.58
0.50
117.70
121.28
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
B
B
B
3
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
B
B
B
3
-3.71
0.60
122.30
118.59
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
B
B
B
3
-4.03
0.60
122.90
118.87
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
B
B
B
3
1.88
0.30
108.30
110.18
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
B
B
B
3
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
B
B
B
3
-4.11
0.60
122.90
118.79
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
4
2.04
0.30
108.30
110.34
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
4
-3.12
0.50
117.00
113.88
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
4
3.45
0.50
117.70
121.15
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
4
-3.91
0.60
118.60
114.69
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
4
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
4
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
4
-3.27
0.50
117.00
113.73
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
4
3.37
0.50
117.70
121.07
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
4
-4.54
0.60
118.60
114.06
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
4
-3.99
0.60
122.30
118.31
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
4
-3.80
0.60
122.90
119.10
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
4
4.19
0.30
108.30
112.49
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
4
-5.31
0.80
105.90
100.59
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
4
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
4
-4.81
0.60
122.30
117.49
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
4
-4.46
0.60
122.90
118.44
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
4
-5.17
0.50
121.30
116.13
A
A
A
C6
N1
C2
DT
DT
DT
9
9
9
N
4
-5.19
0.60
123.70
118.51
A
A
A
C5
C6
N1
DT
DT
DT
9
9
9
N
4
10.46
1.50
120.40
130.86
A
A
A
C6
N1
C1'
DT
DT
DT
9
9
9
N
B
B
B
4
3.38
0.30
108.30
111.68
A
A
A
O4'
C1'
N1
DU
DU
DU
1
1
1
N
B
B
B
4
5.56
0.60
114.90
120.46
A
A
A
N1
C2
N3
DU
DU
DU
1
1
1
N
B
B
B
4
-5.74
0.70
122.20
116.46
A
A
A
N3
C2
O2
DU
DU
DU
1
1
1
N
B
B
B
4
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
B
B
B
4
-4.39
0.60
122.30
117.91
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
B
B
B
4
-4.31
0.60
122.90
118.59
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
B
B
B
4
-5.24
0.80
105.90
100.66
A
A
A
O4'
C1'
C2'
DG
DG
DG
3
3
3
N
B
B
B
4
6.75
0.30
108.30
115.05
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
B
B
B
4
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
B
B
B
4
3.91
0.50
117.70
121.61
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
B
B
B
4
3.82
0.30
108.30
112.12
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
B
B
B
4
-3.97
0.60
122.30
118.33
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
B
B
B
4
-4.20
0.60
122.90
118.70
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
B
B
B
4
-3.70
0.60
122.30
118.60
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
B
B
B
4
-3.99
0.60
122.90
118.91
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
5
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
5
-3.20
0.50
117.00
113.80
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
5
3.54
0.50
117.70
121.24
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
5
-3.99
0.60
118.60
114.61
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
5
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
5
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
5
-3.29
0.50
117.00
113.71
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
5
3.40
0.50
117.70
121.10
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
5
-4.78
0.60
118.60
113.82
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
5
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
-3.79
0.60
122.90
119.11
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
5
4.64
0.30
108.30
112.94
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
5
1.88
0.30
108.30
110.18
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
5
-5.35
0.80
105.90
100.55
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
5
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
5
-4.84
0.60
122.30
117.46
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
5
-4.57
0.60
122.90
118.33
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
5
-5.29
0.50
121.30
116.01
A
A
A
C6
N1
C2
DT
DT
DT
9
9
9
N
5
-3.75
0.60
127.20
123.45
A
A
A
C2
N3
C4
DT
DT
DT
9
9
9
N
5
-5.36
0.60
123.70
118.34
A
A
A
C5
C6
N1
DT
DT
DT
9
9
9
N
5
10.64
1.50
120.40
131.04
A
A
A
C6
N1
C1'
DT
DT
DT
9
9
9
N
B
B
B
5
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DU
DU
DU
1
1
1
N
B
B
B
5
5.68
0.60
114.90
120.58
A
A
A
N1
C2
N3
DU
DU
DU
1
1
1
N
B
B
B
5
-5.98
0.70
122.20
116.22
A
A
A
N3
C2
O2
DU
DU
DU
1
1
1
N
B
B
B
5
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
B
B
B
5
-4.56
0.60
122.30
117.74
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
B
B
B
5
-4.32
0.60
122.90
118.58
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
B
B
B
5
-4.95
0.80
105.90
100.95
A
A
A
O4'
C1'
C2'
DG
DG
DG
3
3
3
N
B
B
B
5
6.71
0.30
108.30
115.01
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
B
B
B
5
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
B
B
B
5
-5.06
0.80
105.90
100.84
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
B
B
B
5
3.84
0.50
117.70
121.54
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
B
B
B
5
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
B
B
B
5
-3.95
0.60
122.30
118.35
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
B
B
B
5
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
B
B
B
5
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
B
B
B
5
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
B
B
B
5
-3.65
0.60
122.30
118.65
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
B
B
B
5
-3.89
0.60
122.90
119.01
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
6
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
6
-3.14
0.50
117.00
113.86
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
6
3.46
0.50
117.70
121.16
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
6
-4.10
0.60
118.60
114.50
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
6
-4.82
0.80
105.90
101.08
A
A
A
O4'
C1'
C2'
DG
DG
DG
2
2
2
N
6
4.31
0.30
108.30
112.61
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
6
3.04
0.50
111.50
114.54
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
6
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
6
-3.16
0.50
117.00
113.84
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
6
3.73
0.50
117.70
121.43
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
6
-3.94
0.60
118.60
114.66
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
6
-4.09
0.60
122.30
118.21
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
6
-3.80
0.60
122.90
119.10
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
6
-5.45
0.80
105.90
100.45
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
6
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
6
-4.70
0.60
122.30
117.60
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
6
-4.52
0.60
122.90
118.38
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
6
-5.18
0.50
121.30
116.12
A
A
A
C6
N1
C2
DT
DT
DT
9
9
9
N
6
-5.16
0.60
123.70
118.54
A
A
A
C5
C6
N1
DT
DT
DT
9
9
9
N
6
-3.62
0.60
122.30
118.68
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
6
10.51
1.50
120.40
130.91
A
A
A
C6
N1
C1'
DT
DT
DT
9
9
9
N
B
B
B
6
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N1
DU
DU
DU
1
1
1
N
B
B
B
6
5.86
0.60
114.90
120.76
A
A
A
N1
C2
N3
DU
DU
DU
1
1
1
N
B
B
B
6
-6.34
0.70
122.20
115.86
A
A
A
N3
C2
O2
DU
DU
DU
1
1
1
N
B
B
B
6
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
B
B
B
6
-4.10
0.60
122.30
118.20
A
A
A
N3
C2
O2
DT
DT
DT
2
2
2
N
B
B
B
6
-3.89
0.60
122.90
119.01
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
B
B
B
6
7.02
0.30
108.30
115.32
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
B
B
B
6
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
B
B
B
6
-5.25
0.80
105.90
100.65
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
B
B
B
6
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
B
B
B
6
3.86
0.50
117.70
121.56
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
B
B
B
6
-4.30
0.60
122.30
118.00
A
A
A
N3
C2
O2
DT
DT
DT
6
6
6
N
B
B
B
6
-3.84
0.60
122.90
119.06
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
B
B
B
6
4.30
0.30
108.30
112.60
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
B
B
B
6
-3.76
0.60
122.30
118.54
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
B
B
B
6
-3.95
0.60
122.90
118.95
A
A
A
C6
C5
C7
DT
DT
DT
9
9
9
N
B
B
1
A
A
N1
C6
DU
DU
1
1
0.102
0.009
1.375
1.477
N
B
B
2
A
A
N1
C6
DU
DU
1
1
0.103
0.009
1.375
1.478
N
B
B
3
A
A
N1
C6
DU
DU
1
1
0.103
0.009
1.375
1.478
N
B
B
4
A
A
N1
C6
DU
DU
1
1
0.101
0.009
1.375
1.476
N
B
B
5
A
A
N1
C6
DU
DU
1
1
0.102
0.009
1.375
1.477
N
B
B
6
A
A
N1
C6
DU
DU
1
1
0.103
0.009
1.375
1.478
N
Structural Basis for Poor Excision from Hairpin DNA: NMR Study
1
N
N
hydrog
WATSON-CRICK
B
A
DA
1
A
N1
DA
1
1_555
A
DT
9
A
N3
DT
18
1_555
hydrog
WATSON-CRICK
B
A
DA
1
A
N6
DA
1
1_555
A
DT
9
A
O4
DT
18
1_555
hydrog
WATSON-CRICK
B
A
DG
2
A
N1
DG
2
1_555
A
DC
8
A
N3
DC
17
1_555
hydrog
WATSON-CRICK
B
A
DG
2
A
N2
DG
2
1_555
A
DC
8
A
O2
DC
17
1_555
hydrog
WATSON-CRICK
B
A
DG
2
A
O6
DG
2
1_555
A
DC
8
A
N4
DC
17
1_555
hydrog
WATSON-CRICK
B
A
DG
3
A
N1
DG
3
1_555
A
DC
7
A
N3
DC
16
1_555
hydrog
WATSON-CRICK
B
A
DG
3
A
N2
DG
3
1_555
A
DC
7
A
O2
DC
16
1_555
hydrog
WATSON-CRICK
B
A
DG
3
A
O6
DG
3
1_555
A
DC
7
A
N4
DC
16
1_555
hydrog
WATSON-CRICK
B
A
DA
4
A
N1
DA
4
1_555
A
DT
6
A
N3
DT
15
1_555
hydrog
WATSON-CRICK
B
A
DA
4
A
N6
DA
4
1_555
A
DT
6
A
O4
DT
15
1_555
hydrog
WATSON-CRICK
B
A
DT
5
A
N3
DT
5
1_555
A
DA
5
A
N1
DA
14
1_555
hydrog
WATSON-CRICK
B
A
DT
5
A
O4
DT
5
1_555
A
DA
5
A
N6
DA
14
1_555
hydrog
WATSON-CRICK
B
A
DC
6
A
N3
DC
6
1_555
A
DG
4
A
N1
DG
13
1_555
hydrog
WATSON-CRICK
B
A
DC
6
A
N4
DC
6
1_555
A
DG
4
A
O6
DG
13
1_555
hydrog
WATSON-CRICK
B
A
DC
6
A
O2
DC
6
1_555
A
DG
4
A
N2
DG
13
1_555
hydrog
WATSON-CRICK
B
A
DC
7
A
N3
DC
7
1_555
A
DG
3
A
N1
DG
12
1_555
hydrog
WATSON-CRICK
B
A
DC
7
A
N4
DC
7
1_555
A
DG
3
A
O6
DG
12
1_555
hydrog
WATSON-CRICK
B
A
DC
7
A
O2
DC
7
1_555
A
DG
3
A
N2
DG
12
1_555
hydrog
TYPE_16_PAIR
B
A
DT
8
A
N3
DT
8
1_555
A
DT
2
A
O2
DT
11
1_555
hydrog
TYPE_16_PAIR
B
A
DT
8
A
O4
DT
8
1_555
A
DT
2
A
N3
DT
11
1_555
DNA
Uracil, Hairpin DNA, Hairpin loop, Double helix, UDG-Uracil interaction, DNA
1IDX
PDB
1
1IDX
1
9
1IDX
1
9
1IDX
B
A
1
1
18