1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Padrta, P.
Stefl, R.
Zidek, L.
Sklenar, 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
NE
J.BIOMOL.NMR
JBNME9
0800
0925-2738
24
1
14
10.1023/A:1020632900961
12449414
Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bond Residual Dipolar Couplings
2002
10.2210/pdb1kr8/pdb
pdb_00001kr8
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
2147.437
5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
1
syn
polymer
no
no
(DG)(DC)(DG)(DA)(DA)(DG)(DC)
GCGAAGC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
-0.889
1
19
A
1
A
7
-0.034
A_DG1:DC7_A
1
1.387
-0.482
0.046
-0.217
18.787
1
19
A
2
A
6
-0.099
A_DC2:DG6_A
2
3.148
0.258
-0.121
-0.153
36.932
9
11
A
3
A
5
18.265
A_DG3:DA5_A
3
-2.720
6.097
1.475
-4.033
2.774
29.402
A
A
1
2
9.135
A
A
7
6
2.873
4.618
0.448
-0.368
AA_DG1DC2:DG6DC7_AA
1
-0.526
1.040
29.040
-1.584
-0.980
3.111
52.148
A
A
2
3
12.747
A
A
6
5
2.945
11.124
-0.199
1.100
AA_DC2DG3:DA5DG6_AA
2
-3.274
3.752
50.930
0.558
0.023
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-12-11
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
_pdbx_nmr_spectrometer.model
RCSB
Y
RCSB
2002-01-09
REL
REL
This sequence occurs naturally in replication origins of phage phiX174, in herpes simplex virus, in E. coli heat-shock gene and rRNA genes.
sample
The structure was determined using triple-resonance NMR spectroscopy in isotropic and liquid crystalline phase.
all calculated structures submitted
14
14
2D NOESY
2D NOESY
E-COSY
DQF-COSY
coupled HSQC
S3E E-COSY
10 mM
6.7
1
atm
303
K
10 mM
6.7
1
atm
277
K
10 mM
6.7
1
atm
303
K
molecular dynamics
7
closest to the average
6mM natural abundance d(GCGAAGC), 10mM phosphate buffer Na, D2O
D2O
6mM natural abundance d(GCGAAGC), 10mM phosphate buffer Na, 90% H2O, 10% D2O
90% H2O/10% D2O
U-15N,13C, 0.5mM d(GCGAAGC), 10mM phosphate buffer Na, 90% H2O, 10% D2O
90% H2O/10% D2O
Bruker
collection
XwinNMR
2.1, 3.0
Bruker
processing
XwinNMR
2.1, 3.0
T. D. Goddard and D. G. Kneller
data analysis
Sparky
3.x
Kollman, Case et. al
structure solution
Amber
6.0
Kollman, Case et. al
refinement
Amber
6.0
500
Bruker
AVANCE
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
G
6
n
6
DG
6
A
C
7
n
7
DC
7
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
DA
4
0.083
SIDE CHAIN
1
A
DA
5
0.081
SIDE CHAIN
2
A
DG
3
0.061
SIDE CHAIN
2
A
DA
4
0.062
SIDE CHAIN
2
A
DA
5
0.100
SIDE CHAIN
2
A
DG
6
0.065
SIDE CHAIN
3
A
DG
3
0.061
SIDE CHAIN
3
A
DA
4
0.078
SIDE CHAIN
3
A
DA
5
0.084
SIDE CHAIN
4
A
DG
3
0.064
SIDE CHAIN
4
A
DA
4
0.062
SIDE CHAIN
4
A
DA
5
0.103
SIDE CHAIN
4
A
DG
6
0.070
SIDE CHAIN
5
A
DA
5
0.096
SIDE CHAIN
5
A
DG
6
0.071
SIDE CHAIN
6
A
DA
4
0.068
SIDE CHAIN
6
A
DA
5
0.083
SIDE CHAIN
7
A
DG
3
0.065
SIDE CHAIN
7
A
DA
5
0.090
SIDE CHAIN
8
A
DG
3
0.064
SIDE CHAIN
8
A
DA
4
0.069
SIDE CHAIN
8
A
DA
5
0.087
SIDE CHAIN
9
A
DA
5
0.090
SIDE CHAIN
9
A
DG
6
0.057
SIDE CHAIN
10
A
DG
3
0.065
SIDE CHAIN
10
A
DA
4
0.059
SIDE CHAIN
10
A
DA
5
0.097
SIDE CHAIN
11
A
DG
3
0.077
SIDE CHAIN
11
A
DA
5
0.113
SIDE CHAIN
11
A
DG
6
0.099
SIDE CHAIN
12
A
DG
3
0.058
SIDE CHAIN
12
A
DA
5
0.096
SIDE CHAIN
13
A
DG
3
0.049
SIDE CHAIN
13
A
DA
5
0.105
SIDE CHAIN
13
A
DG
6
0.081
SIDE CHAIN
14
A
DA
4
0.083
SIDE CHAIN
14
A
DA
5
0.078
SIDE CHAIN
1
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
-6.01
0.80
105.90
99.89
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
1
3.28
0.50
117.70
120.98
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
1
-4.07
0.60
118.60
114.53
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
-11.94
1.90
104.00
92.06
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
1
3.34
0.50
117.70
121.04
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
1
-4.33
0.60
118.60
114.27
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
4.68
0.30
108.30
112.98
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-2.41
0.40
106.40
103.99
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
1
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
2
-5.75
0.80
105.90
100.15
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
2
3.17
0.50
117.70
120.87
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
2
-4.07
0.60
118.60
114.53
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
2
3.29
0.50
117.70
120.99
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
2
-4.21
0.60
118.60
114.39
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
2
3.67
0.30
108.30
111.97
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
2
-2.49
0.40
106.40
103.91
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
3
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
3
-6.02
0.80
105.90
99.88
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
3
3.36
0.50
117.70
121.06
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
3
-4.22
0.60
118.60
114.38
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
3
-12.13
1.90
104.00
91.87
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
3
3.34
0.50
117.70
121.04
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
3
-4.60
0.60
118.60
114.00
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
3
3.92
0.30
108.30
112.22
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
3
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
4
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
4
-5.61
0.80
105.90
100.29
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
4
3.36
0.50
117.70
121.06
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
4
-4.22
0.60
118.60
114.38
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
4
-3.16
0.50
117.00
113.84
A
A
A
C4
C5
C6
DA
DA
DA
5
5
5
N
4
3.52
0.50
117.70
121.22
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
4
-4.45
0.60
118.60
114.15
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
4
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
4
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
5
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
5
-5.78
0.80
105.90
100.12
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
5
3.13
0.50
117.70
120.83
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
5
-4.18
0.60
118.60
114.42
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
5
-13.22
1.90
104.00
90.78
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
5
3.31
0.50
117.70
121.01
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
5
-4.31
0.60
118.60
114.29
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
5
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
5
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
5
-5.29
0.70
108.00
102.71
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
6
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
6
-5.93
0.80
105.90
99.97
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
6
3.30
0.50
117.70
121.00
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
6
-4.28
0.60
118.60
114.32
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
6
-12.54
1.90
104.00
91.46
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
6
3.30
0.50
117.70
121.00
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
6
-4.37
0.60
118.60
114.23
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
6
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
7
-6.10
0.80
105.90
99.80
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
7
-4.26
0.70
121.90
117.64
A
A
A
N3
C2
O2
DC
DC
DC
2
2
2
N
7
3.22
0.50
117.70
120.92
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
7
-4.33
0.60
118.60
114.27
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
7
-12.82
1.90
104.00
91.18
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
7
-3.09
0.50
117.00
113.91
A
A
A
C4
C5
C6
DA
DA
DA
5
5
5
N
7
3.48
0.50
117.70
121.18
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
7
-4.57
0.60
118.60
114.03
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
7
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
7
-2.91
0.40
106.40
103.49
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
8
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
8
-5.98
0.80
105.90
99.92
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
8
3.28
0.50
117.70
120.98
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
8
-4.12
0.60
118.60
114.48
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
8
-11.87
1.90
104.00
92.13
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
8
-3.03
0.50
117.00
113.97
A
A
A
C4
C5
C6
DA
DA
DA
5
5
5
N
8
3.49
0.50
117.70
121.19
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
8
-4.37
0.60
118.60
114.23
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
8
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
8
-2.51
0.40
106.40
103.89
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
9
1.88
0.30
108.30
110.18
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
9
-5.88
0.80
105.90
100.02
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
9
3.13
0.50
117.70
120.83
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
9
-4.09
0.60
118.60
114.51
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
9
-13.04
1.90
104.00
90.96
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
9
3.26
0.50
117.70
120.96
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
9
-4.31
0.60
118.60
114.29
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
9
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
9
-2.58
0.40
106.40
103.82
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
10
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
10
-5.83
0.80
105.90
100.07
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
10
3.09
0.50
117.70
120.79
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
10
-3.94
0.60
118.60
114.66
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
10
-11.83
1.90
104.00
92.17
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
10
3.34
0.50
117.70
121.04
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
10
-4.47
0.60
118.60
114.13
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
10
3.95
0.30
108.30
112.25
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
10
-2.86
0.40
106.40
103.54
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
11
-5.69
0.80
105.90
100.21
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
11
3.07
0.50
117.70
120.77
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
11
-4.11
0.60
118.60
114.49
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
11
-3.19
0.50
117.00
113.81
A
A
A
C4
C5
C6
DA
DA
DA
5
5
5
N
11
3.52
0.50
117.70
121.22
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
11
-4.42
0.60
118.60
114.18
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
11
3.74
0.30
108.30
112.04
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
11
-2.84
0.40
106.40
103.56
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
12
2.28
0.30
108.30
110.58
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
12
-5.91
0.80
105.90
99.99
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
12
3.18
0.50
117.70
120.88
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
12
-4.11
0.60
118.60
114.49
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
12
-12.03
1.90
104.00
91.97
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
12
3.32
0.50
117.70
121.02
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
12
-4.36
0.60
118.60
114.24
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
12
3.62
0.30
108.30
111.92
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
12
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
12
9.07
1.40
114.30
123.37
A
A
A
N1
C1'
C2'
DC
DC
DC
7
7
7
N
12
-5.60
0.70
108.00
102.40
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
13
2.04
0.30
108.30
110.34
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
13
-5.73
0.80
105.90
100.17
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
13
3.10
0.50
117.70
120.80
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
13
-3.92
0.60
118.60
114.68
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
13
-11.56
1.90
104.00
92.44
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
13
-3.14
0.50
117.00
113.86
A
A
A
C4
C5
C6
DA
DA
DA
5
5
5
N
13
3.48
0.50
117.70
121.18
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
13
-4.42
0.60
118.60
114.18
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
13
4.02
0.30
108.30
112.32
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
13
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
14
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
14
-5.90
0.80
105.90
100.00
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
14
3.32
0.50
117.70
121.02
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
14
-4.18
0.60
118.60
114.42
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
14
-12.15
1.90
104.00
91.85
A
A
A
O3'
P
O5'
DA
DA
DA
4
5
5
Y
14
3.42
0.50
117.70
121.12
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
14
-4.52
0.60
118.60
114.08
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
14
3.90
0.30
108.30
112.20
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
14
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
Refinement of d(GCGAAGC) Hairpin Structure Using One-and Two-Bonds Residual Dipolar Couplings
1
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
7
A
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
7
A
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
7
A
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
6
A
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
6
A
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
6
A
N2
DG
6
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DA
5
A
N7
DA
5
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N3
DG
3
1_555
A
DA
5
A
N6
DA
5
1_555
DNA
hairpin, DNA, GA mismatch
1KR8
PDB
1
1KR8
1
7
1KR8
1
7
1KR8
A
1
1
7