1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Johannsen, S.
Duepre, N.
Boehme, D.
Mueller, J.
Sigel, R.K.O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
Ag 1
107.868
SILVER ION
non-polymer
C8 H13 N2 O6 P
264.172
1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazole
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
UK
Nat.Chem.
1755-4330
2
229
234
10.1038/nchem.512
21124482
Solution structure of a DNA double helix with consecutive metal-mediated base pairs.
2010
5015.311
DNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3')
2
syn
polymer
107.868
SILVER ION
3
syn
non-polymer
no
yes
(DT)(DT)(DA)(DA)(DT)(DT)(DT)(D33)(D33)(D33)(DA)(DA)(DA)(DT)(DT)(DA)(DA)
TTAATTTNNNAAATTAA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-2.527
1
20
A
1
B
34
2.110
A_DT1:DA34_B
1
-7.755
-0.389
0.088
-0.084
-1.107
1
20
A
2
B
33
4.022
A_DT2:DA33_B
2
-17.275
-0.125
-0.274
-0.212
-2.918
1
20
A
3
B
32
-1.153
A_DA3:DT32_B
3
-11.114
0.126
0.178
-0.209
-4.120
1
20
A
4
B
31
0.817
A_DA4:DT31_B
4
-11.599
0.138
-0.144
-0.140
-3.736
1
20
A
5
B
30
-2.846
A_DT5:DA30_B
5
-7.230
-0.545
-0.022
-0.169
-2.378
1
20
A
6
B
29
-2.585
A_DT6:DA29_B
6
-12.735
-0.428
-0.030
-0.221
-2.027
1
20
A
7
B
28
-1.476
A_DT7:DA28_B
7
-11.301
-0.376
-0.119
-0.085
1.545
1
20
A
11
B
24
-1.206
A_DA11:DT24_B
8
-11.046
0.342
-0.164
-0.087
1.063
1
20
A
12
B
23
-2.458
A_DA12:DT23_B
9
-11.729
0.447
-0.097
-0.207
3.836
1
20
A
13
B
22
-2.523
A_DA13:DT22_B
10
-7.247
0.546
-0.049
-0.147
3.978
1
20
A
14
B
21
0.791
A_DT14:DA21_B
11
-11.110
-0.169
-0.169
-0.126
2.172
1
20
A
15
B
20
-1.088
A_DT15:DA20_B
12
-10.524
-0.126
0.182
-0.208
1.382
1
20
A
16
B
19
3.709
A_DA16:DT19_B
13
-17.296
0.115
-0.263
-0.226
1.691
1
20
A
17
B
18
2.083
A_DA17:DT18_B
14
-6.810
0.411
0.108
-0.094
3.463
36.639
A
A
1
2
-8.543
B
B
34
33
3.500
-5.351
-0.126
-0.044
AA_DT1DT2:DA33DA34_BB
1
1.579
-2.520
36.226
0.716
0.432
3.420
36.727
A
A
2
3
-4.850
B
B
33
32
3.423
-3.038
-0.095
-0.519
AA_DT2DA3:DT32DA33_BB
2
-6.419
10.248
36.057
-0.386
-0.774
3.245
35.751
A
A
3
4
-0.077
B
B
32
31
3.261
-0.047
-0.072
-0.351
AA_DA3DA4:DT31DT32_BB
3
2.919
-4.759
35.636
-0.565
0.536
3.139
34.519
A
A
4
5
6.147
B
B
31
30
3.233
3.640
0.040
-0.698
AA_DA4DT5:DA30DT31_BB
4
-1.555
2.626
34.298
-1.727
-0.302
3.315
35.540
A
A
5
6
5.785
B
B
30
29
3.341
3.526
-0.155
-0.113
AA_DT5DT6:DA29DA30_BB
5
0.023
-0.037
35.371
-0.711
0.257
3.136
33.615
A
A
6
7
13.961
B
B
29
28
3.321
8.000
-0.271
-0.394
AA_DT6DT7:DA28DA29_BB
6
0.338
-0.591
32.674
-1.992
0.524
3.148
33.826
A
A
11
12
14.536
B
B
24
23
3.341
8.374
0.269
-0.377
AA_DA11DA12:DT23DT24_BB
7
-0.465
0.807
32.799
-2.012
-0.537
3.263
35.425
A
A
12
13
5.408
B
B
23
22
3.287
3.286
0.153
-0.104
AA_DA12DA13:DT22DT23_BB
8
-0.257
0.423
35.276
-0.655
-0.289
3.170
34.399
A
A
13
14
5.949
B
B
22
21
3.261
3.511
-0.049
-0.683
AA_DA13DT14:DA21DT22_BB
9
1.854
-3.142
34.176
-1.694
0.369
3.239
35.867
A
A
14
15
1.097
B
B
21
20
3.265
0.675
0.085
-0.351
AA_DT14DT15:DA20DA21_BB
10
-3.107
5.051
35.731
-0.665
-0.581
3.391
36.604
A
A
15
16
-5.120
B
B
20
19
3.395
-3.198
0.057
-0.524
AA_DT15DA16:DT19DA20_BB
11
6.145
-9.840
35.965
-0.374
0.794
3.481
36.866
A
A
16
17
-8.382
B
B
19
18
3.520
-5.281
0.136
-0.056
AA_DA16DA17:DT18DT19_BB
12
-2.031
3.223
36.444
0.681
-0.511
repository
Initial release
Version format compliance
1
0
2010-02-09
1
1
2011-07-13
NMR data related to NMR solutions structure of modified DNA containing imidazole nucleosides at acidic, neutral and basic pH
NMR solutions structure of modified DNA containing imidazole nucleosides at acidic pH
NMR solutions structure of modified DNA containing imidazole nucleosides at neutral pH
NMR solutions structure of modified DNA containing imidazole nucleosides at basic pH
BMRB
Y
RCSB
2009-01-27
REL
REL
AG
SILVER ION
848
366
15
25
442
structures with the lowest energy
200
20
0.2
0.2
1.06
0.34
2D 1H-1H NOESY
2D 1H-1H TOCSY
2D 1H-13C HSQC
2D 1H-15N HSQC
1D 31P
2D 1H-1H NOESY
0.3-0.5
mM
120
mM
0.9-1.5
mM
0.3-0.5
mM
120
mM
0.9-1.5
mM
0.12
7.2
ambient
298
K
0.12
7.2
ambient
278
K
torsion angle dynamics
1
lowest energy
0.3-0.5 mM DNA (34-MER)-1, 120 mM sodium perchlorate-2, 0.9-1.5 mM SILVER ION-3, 100% D2O
100% D2O
0.3-0.5 mM DNA (34-MER)-4, 120 mM sodium perchlorate-5, 0.9-1.5 mM SILVER ION-6, 90% H2O/10% D2O
90% H2O/10% D2O
Bruker Biospin
processing
TOPSPIN
1.3, 2.0, 2.1
Goddard
chemical shift assignment
SPARKY
3.1
Goddard
data analysis
SPARKY
3.1
Goddard
peak picking
SPARKY
3.1
Guntert, Braun and Wuthrich
structure solution
DYANA
1.5
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR_NIH
2.15
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR_NIH
2.15
700
Bruker
Avance
Bruker Avance
400
Bruker
AV-2
Bruker AV-2
AG
35
2
AG
AG
35
A
AG
36
2
AG
AG
36
A
AG
37
2
AG
AG
37
A
DT
1
n
1
DT
1
A
DT
2
n
2
DT
2
A
DA
3
n
3
DA
3
A
DA
4
n
4
DA
4
A
DT
5
n
5
DT
5
A
DT
6
n
6
DT
6
A
DT
7
n
7
DT
7
A
D33
8
n
8
D33
8
A
D33
9
n
9
D33
9
A
D33
10
n
10
D33
10
A
DA
11
n
11
DA
11
A
DA
12
n
12
DA
12
A
DA
13
n
13
DA
13
A
DT
14
n
14
DT
14
A
DT
15
n
15
DT
15
A
DA
16
n
16
DA
16
A
DA
17
n
17
DA
17
A
DT
18
n
1
DT
18
B
DT
19
n
2
DT
19
B
DA
20
n
3
DA
20
B
DA
21
n
4
DA
21
B
DT
22
n
5
DT
22
B
DT
23
n
6
DT
23
B
DT
24
n
7
DT
24
B
D33
25
n
8
D33
25
B
D33
26
n
9
D33
26
B
D33
27
n
10
D33
27
B
DA
28
n
11
DA
28
B
DA
29
n
12
DA
29
B
DA
30
n
13
DA
30
B
DT
31
n
14
DT
31
B
DT
32
n
15
DT
32
B
DA
33
n
16
DA
33
B
DA
34
n
17
DA
34
B
author_defined_assembly
2
dimeric
A
D33
8
A
N3
D33
8
1_555
A
AG
35
C
AG
AG
1_555
B
D33
27
B
N3
D33
10
1_555
177.6
A
D33
9
A
N3
D33
9
1_555
A
AG
36
D
AG
AG
1_555
B
D33
26
B
N3
D33
9
1_555
179.1
A
D33
10
A
N3
D33
10
1_555
A
AG
37
E
AG
AG
1_555
B
D33
25
B
N3
D33
8
1_555
177.8
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
5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3'
NMR solution structure of metal-modified DNA
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
covale
1.609
A
DT
7
A
O3'
DT
7
1_555
A
D33
8
A
P
D33
8
1_555
covale
1.613
A
D33
8
A
O3'
D33
8
1_555
A
D33
9
A
P
D33
9
1_555
covale
1.612
A
D33
9
A
O3'
D33
9
1_555
A
D33
10
A
P
D33
10
1_555
covale
1.618
A
D33
10
A
O3'
D33
10
1_555
A
DA
11
A
P
DA
11
1_555
covale
1.610
B
DT
24
B
O3'
DT
7
1_555
B
D33
25
B
P
D33
8
1_555
covale
1.611
B
D33
25
B
O3'
D33
8
1_555
B
D33
26
B
P
D33
9
1_555
covale
1.610
B
D33
26
B
O3'
D33
9
1_555
B
D33
27
B
P
D33
10
1_555
covale
1.616
B
D33
27
B
O3'
D33
10
1_555
B
DA
28
B
P
DA
11
1_555
metalc
2.127
A
D33
8
A
N3
D33
8
1_555
A
AG
35
C
AG
AG
1_555
metalc
2.119
A
D33
9
A
N3
D33
9
1_555
A
AG
36
D
AG
AG
1_555
metalc
2.128
A
D33
10
A
N3
D33
10
1_555
A
AG
37
E
AG
AG
1_555
metalc
2.124
B
D33
25
B
N3
D33
8
1_555
A
AG
37
E
AG
AG
1_555
metalc
2.117
B
D33
26
B
N3
D33
9
1_555
A
AG
36
D
AG
AG
1_555
metalc
2.123
B
D33
27
B
N3
D33
10
1_555
A
AG
35
C
AG
AG
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
34
B
N1
DA
17
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
34
B
N6
DA
17
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
33
B
N1
DA
16
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
33
B
N6
DA
16
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
32
B
N3
DT
15
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
32
B
O4
DT
15
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
31
B
N3
DT
14
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
31
B
O4
DT
14
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
30
B
N1
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
30
B
N6
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
29
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
29
B
N6
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
28
B
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
28
B
N6
DA
11
1_555
hydrog
WATSON-CRICK
A
DA
11
A
N1
DA
11
1_555
B
DT
24
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
11
A
N6
DA
11
1_555
B
DT
24
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N1
DA
12
1_555
B
DT
23
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N6
DA
12
1_555
B
DT
23
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N1
DA
13
1_555
B
DT
22
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
13
A
N6
DA
13
1_555
B
DT
22
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DT
14
A
N3
DT
14
1_555
B
DA
21
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
14
A
O4
DT
14
1_555
B
DA
21
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
15
A
N3
DT
15
1_555
B
DA
20
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
15
A
O4
DT
15
1_555
B
DA
20
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DA
16
A
N1
DA
16
1_555
B
DT
19
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
16
A
N6
DA
16
1_555
B
DT
19
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
17
A
N1
DA
17
1_555
B
DT
18
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
17
A
N6
DA
17
1_555
B
DT
18
B
O4
DT
1
1_555
DNA
DNA, artificial nucleobase, imidazole nucleoside, Ag+
2KE8
PDB
1
2KE8
TTAATTTXXXAAATTAA
1
17
2KE8
1
17
2KE8
A
1
1
17
18
34
2KE8
18
34
2KE8
B
1
1
17
BINDING SITE FOR RESIDUE AG A 35
Software
2
BINDING SITE FOR RESIDUE AG A 36
Software
2
BINDING SITE FOR RESIDUE AG A 37
Software
2
A
D33
8
A
D33
8
2
1_555
B
D33
27
B
D33
10
2
1_555
A
D33
9
A
D33
9
2
1_555
B
D33
26
B
D33
9
2
1_555
A
D33
10
A
D33
10
2
1_555
B
D33
25
B
D33
8
2
1_555