1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kumbhar, S.
Johannsen, S.
Sigel, R.K.
Waller, M.P.
Mueller, J.
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
US
J.Inorg.Biochem.
JIBIDJ
0525
0162-0134
127
203
210
10.1016/j.jinorgbio.2013.03.009
23622950
A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.
2013
10.2210/pdb2m54/pdb
pdb_00002m54
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
3.556
1
20
A
1
B
34
6.435
A_DT1:DA34_B
1
-7.794
-0.344
-0.310
-0.143
7.008
1
20
A
2
B
33
2.489
A_DT2:DA33_B
2
-12.359
0.051
-0.098
-0.128
-1.290
1
20
A
3
B
32
0.065
A_DA3:DT32_B
3
-17.261
0.040
0.008
-0.103
-3.600
1
20
A
4
B
31
2.365
A_DA4:DT31_B
4
-14.100
0.106
-0.381
-0.117
-5.432
1
20
A
5
B
30
1.363
A_DT5:DA30_B
5
-12.902
0.071
0.240
-0.099
-2.362
1
20
A
6
B
29
0.483
A_DT6:DA29_B
6
-11.082
-0.138
-0.087
-0.152
-4.906
1
20
A
7
B
28
1.688
A_DT7:DA28_B
7
-11.110
-0.387
-0.256
-0.110
4.940
1
20
A
11
B
24
1.564
A_DA11:DT24_B
8
-11.055
0.361
-0.251
-0.093
2.364
1
20
A
12
B
23
0.320
A_DA12:DT23_B
9
-10.951
0.153
-0.133
-0.139
6.131
1
20
A
13
B
22
1.560
A_DA13:DT22_B
10
-12.394
-0.046
0.234
-0.088
3.844
1
20
A
14
B
21
2.208
A_DT14:DA21_B
11
-13.948
-0.071
-0.378
-0.140
1.082
1
20
A
15
B
20
0.082
A_DT15:DA20_B
12
-17.870
-0.045
0.032
-0.143
-7.034
1
20
A
16
B
19
2.702
A_DA16:DT19_B
13
-12.695
-0.048
-0.126
-0.154
-3.669
1
20
A
17
B
18
6.334
A_DA17:DT18_B
14
-7.710
0.329
-0.302
-0.154
3.387
36.855
A
A
1
2
-0.183
B
B
34
33
3.385
-0.116
-0.153
-0.183
AA_DT1DT2:DA33DA34_BB
1
-0.520
0.822
36.851
-0.273
0.169
3.284
31.930
A
A
2
3
9.331
B
B
33
32
3.442
5.111
-0.108
-0.757
AA_DT2DA3:DT32DA33_BB
2
-1.189
2.171
31.507
-2.335
-0.026
3.062
34.427
A
A
3
4
12.887
B
B
32
31
3.179
7.556
0.199
-0.222
AA_DA3DA4:DT31DT32_BB
3
3.564
-6.079
33.428
-1.515
0.201
3.033
36.896
A
A
4
5
7.621
B
B
31
30
3.188
4.803
0.331
-0.667
AA_DA4DT5:DA30DT31_BB
4
-3.588
5.693
36.422
-1.676
-0.988
2.880
34.946
A
A
5
6
11.669
B
B
30
29
3.017
6.956
-0.079
-0.332
AA_DT5DT6:DA29DA30_BB
5
2.823
-4.736
34.154
-1.512
0.521
3.229
32.174
A
A
6
7
8.625
B
B
29
28
3.318
4.762
-0.201
-0.280
AA_DT6DT7:DA28DA29_BB
6
1.596
-2.891
31.790
-1.362
0.650
3.237
32.219
A
A
11
12
8.345
B
B
24
23
3.319
4.614
0.203
-0.277
AA_DA11DA12:DT23DT24_BB
7
-1.392
2.516
31.866
-1.328
-0.617
2.856
35.034
A
A
12
13
12.079
B
B
23
22
2.997
7.215
0.097
-0.321
AA_DA12DA13:DT22DT23_BB
8
-2.759
4.618
34.198
-1.516
-0.536
3.059
36.901
A
A
13
14
7.559
B
B
22
21
3.211
4.766
-0.349
-0.658
AA_DA13DT14:DA21DT22_BB
9
3.457
-5.484
36.444
-1.661
1.003
3.054
34.465
A
A
14
15
13.557
B
B
21
20
3.186
7.949
-0.190
-0.234
AA_DT14DT15:DA20DA21_BB
10
-3.677
6.270
33.366
-1.593
-0.234
3.298
32.039
A
A
15
16
8.923
B
B
20
19
3.445
4.905
0.101
-0.736
AA_DT15DA16:DT19DA20_BB
11
1.334
-2.426
31.644
-2.251
0.066
3.375
36.897
A
A
16
17
-0.080
B
B
19
18
3.374
-0.051
0.142
-0.189
AA_DA16DA17:DT18DT19_BB
12
0.112
-0.177
36.896
-0.291
-0.209
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Other
1
0
2013-05-15
1
1
2013-09-25
1
2
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
NMR data related to NMR solution structure of metal-modified DNA
NMR solution structure of metal-modified DNA
NMR solution structure of modified DNA containing imidazole nucleosides at neutral pH
BMRB
Y
RCSB
2013-02-13
REL
REL
REL
REL
AG
SILVER ION
34
34
28
28
34
34
0
848
366
15
25
442
56
structures with the lowest energy
200
20
0.2
0.2
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
0.9-1.5
mM
120
mM
0.3-0.5
mM
0.9-1.5
mM
120
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 ds DNA, 0.9-1.5 mM SILVER ION, 120 mM sodium perchlorate, 100% D2O
100% D2O
0.3-0.5 mM ds DNA, 0.9-1.5 mM SILVER ION, 120 mM sodium perchlorate, 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
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
AVANCE
Bruker Avance
AG
35
2
AG
AG
101
A
AG
36
2
AG
AG
102
A
AG
37
2
AG
AG
103
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
101
C
AG
AG
1_555
B
D33
27
B
N3
D33
10
1_555
176.7
A
D33
9
A
N3
D33
9
1_555
A
AG
102
D
AG
AG
1_555
B
D33
26
B
N3
D33
9
1_555
179.9
A
D33
10
A
N3
D33
10
1_555
A
AG
103
E
AG
AG
1_555
B
D33
25
B
N3
D33
8
1_555
176.6
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
Refined 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
both
A
DT
7
A
O3'
DT
7
1_555
A
D33
8
A
P
D33
8
1_555
covale
1.607
both
A
D33
8
A
O3'
D33
8
1_555
A
D33
9
A
P
D33
9
1_555
covale
1.608
both
A
D33
9
A
O3'
D33
9
1_555
A
D33
10
A
P
D33
10
1_555
covale
1.611
both
A
D33
10
A
O3'
D33
10
1_555
A
DA
11
A
P
DA
11
1_555
covale
1.609
both
B
DT
24
B
O3'
DT
7
1_555
B
D33
25
B
P
D33
8
1_555
covale
1.607
both
B
D33
25
B
O3'
D33
8
1_555
B
D33
26
B
P
D33
9
1_555
covale
1.608
both
B
D33
26
B
O3'
D33
9
1_555
B
D33
27
B
P
D33
10
1_555
covale
1.611
both
B
D33
27
B
O3'
D33
10
1_555
B
DA
28
B
P
DA
11
1_555
metalc
2.137
A
D33
8
A
N3
D33
8
1_555
A
AG
101
C
AG
AG
1_555
metalc
2.139
A
D33
9
A
N3
D33
9
1_555
A
AG
102
D
AG
AG
1_555
metalc
2.130
A
D33
10
A
N3
D33
10
1_555
A
AG
103
E
AG
AG
1_555
metalc
2.130
A
AG
101
C
AG
AG
1_555
B
D33
27
B
N3
D33
10
1_555
metalc
2.140
A
AG
102
D
AG
AG
1_555
B
D33
26
B
N3
D33
9
1_555
metalc
2.136
A
AG
103
E
AG
AG
1_555
B
D33
25
B
N3
D33
8
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
2M54
PDB
1
2M54
1
17
2M54
1
17
2M54
A
1
1
17
18
34
2M54
18
34
2M54
B
1
1
17
BINDING SITE FOR RESIDUE AG A 101
A
AG
101
Software
4
BINDING SITE FOR RESIDUE AG A 102
A
AG
102
Software
6
BINDING SITE FOR RESIDUE AG A 103
A
AG
103
Software
4
A
D33
8
A
D33
8
4
1_555
A
D33
9
A
D33
9
4
1_555
A
AG
102
D
AG
4
1_555
B
D33
27
B
D33
10
4
1_555
A
D33
9
A
D33
9
6
1_555
A
D33
10
A
D33
10
6
1_555
A
AG
101
C
AG
6
1_555
A
AG
103
E
AG
6
1_555
B
D33
26
B
D33
9
6
1_555
B
D33
27
B
D33
10
6
1_555
A
D33
10
A
D33
10
4
1_555
A
AG
102
D
AG
4
1_555
B
D33
25
B
D33
8
4
1_555
B
D33
26
B
D33
9
4
1_555