1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Schmidt, O.P.
Jurt, S.
Johannsen, S.
Karimi, A.
Sigel, R.K.O.
Luedtke, N.W.
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
Hg 2
200.590
MERCURY (II) ION
non-polymer
UK
Nat Commun
2041-1723
10
4818
4818
10.1038/s41467-019-12440-x
31645548
Concerted dynamics of metallo-base pairs in an A/B-form helical transition.
2019
0000-0001-7973-8996
4255.778
DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major
2
syn
polymer
200.590
MERCURY (II) ION
2
syn
non-polymer
no
no
(DC)(DG)(DT)(DC)(DT)(DC)(DA)(DT)(DG)(DA)(DT)(DA)(DC)(DG)
CGTCTCATGATACG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
0.955
1
19
A
1
B
28
3.081
A_DC1:DG28_B
1
-8.233
0.360
-0.165
-0.196
4.851
1
19
A
2
B
27
-1.494
A_DG2:DC27_B
2
-5.618
0.094
0.128
-0.212
-0.868
1
20
A
3
B
26
-0.285
A_DT3:DA26_B
3
-13.461
0.033
-0.043
-0.188
-4.534
1
20
A
5
B
24
0.212
A_DT5:DA24_B
4
-20.410
-0.072
0.139
-0.153
-3.347
1
19
A
6
B
23
-0.522
A_DC6:DG23_B
5
-11.118
0.211
0.135
-0.238
-1.111
1
20
A
7
B
22
-2.534
A_DA7:DT22_B
6
-11.301
0.165
0.055
-0.092
1.521
1
20
A
8
B
21
-2.528
A_DT8:DA21_B
7
-10.773
-0.176
0.042
-0.095
3.792
1
19
A
9
B
20
-0.591
A_DG9:DC20_B
8
-11.153
-0.219
0.155
-0.242
4.330
1
20
A
10
B
19
0.182
A_DA10:DT19_B
9
-20.640
0.059
0.125
-0.151
0.574
1
20
A
12
B
17
-0.164
A_DA12:DT17_B
10
-13.519
-0.027
-0.064
-0.180
-4.774
1
19
A
13
B
16
-1.391
A_DC13:DG16_B
11
-6.074
-0.066
0.106
-0.205
-0.607
1
19
A
14
B
15
3.275
A_DG14:DC15_B
12
-8.213
-0.358
-0.157
-0.190
3.423
36.114
A
A
1
2
9.800
B
B
28
27
3.392
6.047
-0.079
0.465
AA_DC1DG2:DC27DG28_BB
1
-1.545
2.503
35.588
-0.146
-0.102
3.250
32.317
A
A
2
3
10.990
B
B
27
26
3.425
6.080
0.019
-0.621
AA_DG2DT3:DA26DC27_BB
2
1.603
-2.897
31.716
-2.225
0.258
5.775
72.107
A
A
3
5
11.224
B
B
26
24
5.981
13.153
-0.082
-0.778
AA_DT3DT5:DA24DA26_BB
3
2.905
-2.479
71.006
-1.457
0.245
3.206
36.924
A
A
5
6
1.530
B
B
24
23
3.211
0.969
-0.053
-0.133
AA_DT5DC6:DG23DA24_BB
4
0.395
-0.623
36.910
-0.338
0.137
3.230
37.614
A
A
6
7
9.427
B
B
23
22
3.226
6.053
0.150
0.268
AA_DC6DA7:DT22DG23_BB
5
0.607
-0.945
37.136
-0.366
-0.155
3.121
31.752
A
A
7
8
-5.771
B
B
22
21
3.066
-3.152
0.000
-0.716
AA_DA7DT8:DA21DT22_BB
6
0.079
-0.144
31.600
-0.761
0.014
3.235
37.613
A
A
8
9
9.117
B
B
21
20
3.229
5.855
-0.148
0.269
AA_DT8DG9:DC20DA21_BB
7
-0.762
1.187
37.163
-0.341
0.131
3.232
36.894
A
A
9
10
1.737
B
B
20
19
3.237
1.099
0.058
-0.137
AA_DG9DA10:DT19DC20_BB
8
-0.118
0.187
36.878
-0.363
-0.107
5.774
72.121
A
A
10
12
11.257
B
B
19
17
5.980
13.194
0.091
-0.771
AA_DA10DA12:DT17DT19_BB
9
-2.875
2.453
71.014
-1.453
-0.251
3.236
32.447
A
A
12
13
10.945
B
B
17
16
3.409
6.079
-0.007
-0.617
AA_DA12DC13:DG16DT17_BB
10
-1.479
2.662
31.854
-2.200
-0.254
3.421
35.884
A
A
13
14
10.043
B
B
16
15
3.388
6.157
0.089
0.471
AA_DC13DG14:DC15DG16_BB
11
1.436
-2.342
35.340
-0.160
0.071
citation
citation_author
pdbx_database_related
repository
Initial release
Database references
1
0
2019-10-09
1
1
2019-11-13
_citation.country
_citation.journal_abbrev
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.year
Switzerland
Swiss National Science Foundation
165949
Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species)
N
PDBE
Y
PDBE
2018-03-11
REL
REL
REL
HG
MERCURY (II) ION
32630
synthetic construct
sample
1
14
structures with the lowest energy
200
20
isotropic
2
2D 1H-1H NOESY
isotropic
1
2D 1H-1H NOESY
isotropic
1
2D 1H-1H COSY
isotropic
1
2D 1H-1H TOCSY
isotropic
1
2D 1H-13C HSQC aliphatic
isotropic
1
2D 1H-13C HSQC aromatic
isotropic
1
2D 1H-1H NOESY
0.4
mM
none
1.2
mM
none
0.4
mM
none
1.2
mM
none
50
mM
conditions_2
7.75
pH
ambient
atm
277
K
50
mM
conditions_3
7.35
pD
ambient
atm
298
K
2000 preliminary structures were calculated. The 20 lowest energy structures were selected and subsequently refined. Of the 200 refined conformers calculated the 20 lowest energy structures were chosen
simulated annealing
1
fewest violations
0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 90% H2O/10% D2O
1_H2O/D2O
90% H2O/10% D2O
solution
0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O
1_D2O
100% D2O
solution
Bruker Biospin
collection
TopSpin
4.0.0.b.16
G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra
structure calculation
Xplor-NIH
2.46
Goddard
chemical shift assignment
Sparky
Goddard
peak picking
Sparky
G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra
refinement
Xplor-NIH
2.46
600
Bruker
AVANCE
700
Bruker
AVANCE
HG
30
2
HG
HG
101
A
HG
29
2
HG
HG
102
A
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DT
3
n
3
DT
3
A
DC
4
n
4
DC
4
A
DT
5
n
5
DT
5
A
DC
6
n
6
DC
6
A
DA
7
n
7
DA
7
A
DT
8
n
8
DT
8
A
DG
9
n
9
DG
9
A
DA
10
n
10
DA
10
A
DT
11
n
11
DT
11
A
DA
12
n
12
DA
12
A
DC
13
n
13
DC
13
A
DG
14
n
14
DG
14
A
DC
15
n
1
DC
15
B
DG
16
n
2
DG
16
B
DT
17
n
3
DT
17
B
DC
18
n
4
DC
18
B
DT
19
n
5
DT
19
B
DC
20
n
6
DC
20
B
DA
21
n
7
DA
21
B
DT
22
n
8
DT
22
B
DG
23
n
9
DG
23
B
DA
24
n
10
DA
24
B
DT
25
n
11
DT
25
B
DA
26
n
12
DA
26
B
DC
27
n
13
DC
27
B
DG
28
n
14
DG
28
B
author_and_software_defined_assembly
PISA
2
dimeric
We performed CD spectroscopy and concentration dependant thermal melting temperature experiments to confirm formation of B-form duplex DNA. We used site-selective 15N-labeling and 199Hg-enriched Hg(ClO4)2 to determine the binding site.
none
1660
-64
5140
A
DC
4
A
N3
DC
4
1_555
A
HG
102
D
HG
HG
1_555
B
DT
25
B
N3
DT
11
1_555
178.8
A
DT
11
A
N3
DT
11
1_555
A
HG
101
C
HG
HG
1_555
B
DC
18
B
N3
DC
4
1_555
178.8
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
N
DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major
Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species)
1
N
N
1
N
N
2
N
N
2
N
N
metalc
2.044
A
DC
4
A
N3
DC
4
1_555
A
HG
102
D
HG
HG
1_555
metalc
2.047
A
DT
11
A
N3
DT
11
1_555
A
HG
101
C
HG
HG
1_555
metalc
2.047
B
DC
18
B
N3
DC
4
1_555
A
HG
101
C
HG
HG
1_555
metalc
2.045
B
DT
25
B
N3
DT
11
1_555
A
HG
102
D
HG
HG
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
28
B
N1
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
28
B
O6
DG
14
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
28
B
N2
DG
14
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
27
B
N3
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
27
B
O2
DC
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
27
B
N4
DC
13
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
26
B
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
26
B
N6
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
24
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
24
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
23
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
23
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
23
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
22
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
22
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
21
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
21
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
20
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
20
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
20
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
B
DT
19
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
B
DT
19
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N1
DA
12
1_555
B
DT
17
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
12
A
N6
DA
12
1_555
B
DT
17
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N3
DC
13
1_555
B
DG
16
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
13
A
N4
DC
13
1_555
B
DG
16
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
13
A
O2
DC
13
1_555
B
DG
16
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
14
A
N1
DG
14
1_555
B
DC
15
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
14
A
N2
DG
14
1_555
B
DC
15
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
14
A
O6
DG
14
1_555
B
DC
15
B
N4
DC
1
1_555
DNA
metallated duplex DNA, B-form helix, A-form helix, mercury(II)-mediated base pair, DNA
6FY6
PDB
1
1
6FY6
1
14
6FY6
1
14
6FY6
A
1
1
14
15
28
6FY6
15
28
6FY6
B
1
1
14
binding site for residue HG A 101
A
HG
101
Software
5
binding site for residue HG A 102
A
HG
102
Software
5
A
DA
10
A
DA
10
5
1_555
A
DT
11
A
DT
11
5
1_555
A
DA
12
A
DA
12
5
1_555
B
DC
18
B
DC
4
5
1_555
B
DT
19
B
DT
5
5
1_555
A
DC
4
A
DC
4
5
1_555
A
DT
5
A
DT
5
5
1_555
B
DA
24
B
DA
10
5
1_555
B
DT
25
B
DT
11
5
1_555
B
DA
26
B
DA
12
5
1_555