1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Klewer, D.A.
Hoskins, A.
Davisson, V.J.
Bergstrom, D.E.
LiWang, A.C.
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 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
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
28
4514
4522
10.1093/nar/28.22.4514
11071940
NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control.
2000
10.2210/pdb1dk9/pdb
pdb_00001dk9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2739.824
5'-D(CP*AP*TP*GP*AP*GP*TP*AP*CP*)-3'
1
syn
polymer
2730.810
5'-D(GP*TP*AP*CP*TP*CP*AP*TP*GP*)-3'
1
syn
polymer
no
no
(DC)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DC)
CATGAGTAC
A
polydeoxyribonucleotide
no
no
(DG)(DT)(DA)(DC)(DT)(DC)(DA)(DT)(DG)
GTACTCATG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
11.032
1
19
A
1
B
18
0.988
A_DC1:DG18_B
1
-20.539
0.299
0.156
-0.468
3.758
1
20
A
2
B
17
4.559
A_DA2:DT17_B
2
-9.696
0.108
0.360
-0.357
1.353
1
20
A
3
B
16
10.682
A_DT3:DA16_B
3
-12.621
0.124
0.573
-0.326
3.994
1
19
A
4
B
15
-0.372
A_DG4:DC15_B
4
-1.764
-0.157
0.084
-0.485
-1.271
1
20
A
5
B
14
3.075
A_DA5:DT14_B
5
-7.882
0.296
-0.111
-0.370
-5.926
1
19
A
6
B
13
2.040
A_DG6:DC13_B
6
-10.084
-0.273
0.136
-0.508
-15.253
1
20
A
7
B
12
-1.035
A_DT7:DA12_B
7
-0.937
-0.083
0.069
-0.359
-15.567
1
20
A
8
B
11
1.908
A_DA8:DT11_B
8
-3.001
0.043
-0.264
-0.377
-11.700
1
19
A
9
B
10
-0.778
A_DC9:DG10_B
9
2.336
0.324
0.302
-0.466
2.288
32.392
A
A
1
2
21.018
B
B
18
17
2.928
11.459
-0.296
-1.368
AA_DC1DA2:DT17DG18_BB
1
-3.550
6.512
30.144
-4.125
0.012
3.201
37.445
A
A
2
3
-8.652
B
B
17
16
3.109
-5.535
0.290
-0.913
AA_DA2DT3:DA16DT17_BB
2
-0.842
1.316
37.038
-0.717
-0.559
2.747
37.904
A
A
3
4
2.044
B
B
16
15
2.799
1.327
-0.248
-0.825
AA_DT3DG4:DC15DA16_BB
3
2.620
-4.038
37.794
-1.414
0.667
3.023
40.752
A
A
4
5
5.086
B
B
15
14
3.104
3.535
0.103
-0.842
AA_DG4DA5:DT14DC15_BB
4
2.900
-4.172
40.506
-1.576
0.153
2.952
34.973
A
A
5
6
5.928
B
B
14
13
3.075
3.553
-0.182
-1.149
AA_DA5DG6:DC13DT14_BB
5
-2.708
4.518
34.696
-2.408
-0.075
3.390
42.940
A
A
6
7
-7.579
B
B
13
12
3.308
-5.527
-0.119
-1.051
AA_DG6DT7:DA12DC13_BB
6
3.786
-5.191
42.438
-0.871
0.550
2.850
40.176
A
A
7
8
11.101
B
B
12
11
2.988
7.570
0.385
-0.621
AA_DT7DA8:DT11DA12_BB
7
4.238
-6.214
39.265
-1.682
-0.125
3.009
30.090
A
A
8
9
-4.014
B
B
11
10
3.047
-2.074
0.252
-0.624
AA_DA8DC9:DG10DT11_BB
8
-4.660
9.018
29.665
-0.807
-1.374
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
1999-12-16
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Residue 14 is replaced by 3-nitropyrrole
RCSB
Y
RCSB
1999-12-06
REL
THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED
sample
THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED
sample
1
2D NOESY
DQF-COSY
7
ambient
278
K
4.5mM duplex, 100mM NaCl, 10mM NaOP, 1mM EDTA
95% H2O/5% D2O
Liu
iterative matrix relaxation
CORMA
5.2
Borgias, James
iterative matrix relaxation
MARDIGRAS
5.2
Delaglio
processing
NMRPipe
7.1
Varian
collection
VNMR
6.1B
Brunger
refinement
X-PLOR
V3.840
Garrett
data analysis
PIPP
4.2.7
600
Varian
INOVA
CYT
1
n
1
DC
1
A
ADE
2
n
2
DA
2
A
THY
3
n
3
DT
3
A
GUA
4
n
4
DG
4
A
ADE
5
n
5
DA
5
A
GUA
6
n
6
DG
6
A
THY
7
n
7
DT
7
A
ADE
8
n
8
DA
8
A
CYT
9
n
9
DC
9
A
GUA
10
n
1
DG
10
B
THY
11
n
2
DT
11
B
ADE
12
n
3
DA
12
B
CYT
13
n
4
DC
13
B
THY
14
n
5
DT
14
B
CYT
15
n
6
DC
15
B
ADE
16
n
7
DA
16
B
THY
17
n
8
DT
17
B
GUA
18
n
9
DG
18
B
author_defined_assembly
2
dimeric
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
B
H21
O2
DG
DC
6
13
1.40
1
A
B
H21
O2
DG
DC
4
15
1.47
1
A
B
O2
H21
DC
DG
1
18
1.48
1
A
B
O2
H21
DC
DG
9
10
1.50
1
A
B
O6
H41
DG
DC
4
15
1.50
1
A
B
H41
O6
DC
DG
9
10
1.54
1
A
B
H1
N3
DG
DC
6
13
1.54
1
A
B
H1
N3
DG
DC
4
15
1.55
1
A
B
N1
H3
DA
DT
8
11
1.56
1
A
B
N1
H3
DA
DT
5
14
1.56
1
A
B
N1
H3
DA
DT
2
17
1.58
1
A
B
O6
H41
DG
DC
6
13
1.58
1
A
B
N3
H1
DC
DG
1
18
1.58
1
A
B
O4
H61
DT
DA
7
12
1.59
1
A
B
H3
N1
DT
DA
7
12
1.59
1
3.62
0.30
108.30
111.92
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
3.31
0.50
113.10
116.41
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
4.61
0.30
108.30
112.91
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
3.80
0.30
108.30
112.10
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
3.63
0.50
113.10
116.73
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
1
-4.77
0.70
108.00
103.23
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
-5.46
0.80
105.90
100.44
A
A
A
O4'
C1'
C2'
DC
DC
DC
9
9
9
N
1
5.93
0.30
108.30
114.23
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.49
0.50
113.10
116.59
B
B
B
N7
C8
N9
DG
DG
DG
10
10
10
N
1
7.72
0.30
108.30
116.02
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-6.21
0.60
122.90
116.69
B
B
B
C6
C5
C7
DT
DT
DT
11
11
11
N
1
1.90
0.30
108.30
110.20
B
B
B
O4'
C1'
N9
DA
DA
DA
12
12
12
N
1
3.52
0.30
108.30
111.82
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.33
0.50
113.80
117.13
B
B
B
N7
C8
N9
DA
DA
DA
16
16
16
N
1
-3.63
0.60
122.90
119.27
B
B
B
C6
C5
C7
DT
DT
DT
17
17
17
N
1
-6.03
1.00
110.10
104.07
B
B
B
C1'
O4'
C4'
DG
DG
DG
18
18
18
N
1
2.55
0.30
108.30
110.85
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
3.08
0.50
113.10
116.18
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
A
A
C5
C7
DT
DT
7
7
0.046
0.006
1.496
1.542
N
1
B
B
C5
C7
DT
DT
17
17
0.038
0.006
1.496
1.534
N
SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
18
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
18
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
18
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
17
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
17
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
16
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
16
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
15
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
15
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
15
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
14
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
14
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
13
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
13
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
13
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
12
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
12
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
11
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
11
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
10
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
10
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
10
B
N2
DG
1
1_555
DNA
DNA, DUPLEX
1DK9
PDB
1
1DK9
1DK9
PDB
2
1DK9
1
9
1DK9
1
9
1DK9
A
1
1
9
10
18
1DK9
10
18
1DK9
B
2
1
9
1
P 1