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')_minor
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
-2.420
1
19
A
1
B
28
4.543
A_DC1:DG28_B
1
-15.325
0.747
0.191
-0.232
-0.611
1
19
A
2
B
27
0.453
A_DG2:DC27_B
2
-11.942
-0.008
0.003
-0.188
0.941
1
20
A
3
B
26
-2.049
A_DT3:DA26_B
3
-14.997
-0.200
-0.099
-0.245
-0.564
1
20
A
5
B
24
-4.975
A_DT5:DA24_B
4
-17.221
-0.025
-0.038
-0.181
-6.587
1
19
A
6
B
23
2.054
A_DC6:DG23_B
5
-10.686
0.195
-0.171
-0.192
-1.796
1
20
A
7
B
22
-3.147
A_DA7:DT22_B
6
-8.923
0.502
-0.077
-0.131
1.840
1
20
A
8
B
21
-3.280
A_DT8:DA21_B
7
-8.451
-0.533
-0.060
-0.105
6.444
1
19
A
9
B
20
2.123
A_DG9:DC20_B
8
-10.757
-0.203
-0.150
-0.182
-0.089
1
20
A
10
B
19
-4.563
A_DA10:DT19_B
9
-16.769
0.039
-0.063
-0.171
-0.747
1
20
A
12
B
17
-1.686
A_DA12:DT17_B
10
-15.097
0.204
-0.100
-0.249
0.745
1
19
A
13
B
16
0.473
A_DC13:DG16_B
11
-11.637
0.016
-0.025
-0.213
2.739
1
19
A
14
B
15
4.511
A_DG14:DC15_B
12
-15.041
-0.761
0.190
-0.261
3.368
35.353
A
A
1
2
7.734
B
B
28
27
3.346
4.682
-0.106
0.380
AA_DC1DG2:DC27DG28_BB
1
-1.737
2.869
35.010
-0.087
-0.089
3.099
31.825
A
A
2
3
5.299
B
B
27
26
3.173
2.902
-0.406
-0.744
AA_DG2DT3:DA26DC27_BB
2
-0.409
0.747
31.694
-1.866
0.669
6.112
71.121
A
A
3
5
5.299
B
B
26
24
6.244
6.155
-0.340
-1.634
AA_DT3DT5:DA24DA26_BB
3
-4.081
3.514
70.786
-1.806
0.027
3.367
36.994
A
A
5
6
9.174
B
B
24
23
3.426
5.798
0.176
-0.125
AA_DT5DC6:DG23DA24_BB
4
-0.166
0.262
36.552
-1.012
-0.301
3.394
39.162
A
A
6
7
15.034
B
B
23
22
3.285
9.974
-0.319
0.845
AA_DC6DA7:DT22DG23_BB
5
-0.302
0.454
37.917
0.019
0.438
3.075
32.195
A
A
7
8
4.128
B
B
22
21
3.118
2.287
-0.005
-0.510
AA_DA7DT8:DA21DT22_BB
6
-0.203
0.367
32.115
-1.306
-0.025
3.397
39.267
A
A
8
9
14.682
B
B
21
20
3.289
9.770
0.320
0.839
AA_DT8DG9:DC20DA21_BB
7
0.367
-0.552
38.077
0.038
-0.431
3.389
37.002
A
A
9
10
9.028
B
B
20
19
3.447
5.708
-0.162
-0.115
AA_DG9DA10:DT19DC20_BB
8
0.439
-0.694
36.572
-0.989
0.317
6.082
71.003
A
A
10
12
5.538
B
B
19
17
6.218
6.423
0.352
-1.612
AA_DA10DA12:DT17DT19_BB
9
4.032
-3.477
70.650
-1.806
-0.041
3.111
31.970
A
A
12
13
5.199
B
B
17
16
3.180
2.860
0.395
-0.727
AA_DA12DC13:DG16DT17_BB
10
0.640
-1.163
31.839
-1.818
-0.606
3.361
35.422
A
A
13
14
8.038
B
B
16
15
3.340
4.874
0.101
0.371
AA_DC13DG14:DC15DG16_BB
11
1.482
-2.443
35.065
-0.127
0.058
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 (minor 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 COSY
isotropic
1
2D 1H-1H TOCSY
isotropic
1
2D 1H-13C HSQC aliphatic
isotropic
1
2D 1H-13C HSQC aromatic
0.4
mM
none
1.2
mM
none
50
mM
conditions_3
7.35
pD
ambient
atm
298
K
2000 preliminary structures were calculated. The 20 lowest energy structures were subsequently refined. From the 200 calculated refined conformers the 20 lowest energy structures were chosen
simulated annealing
1
fewest violations
0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O
1_D2O
100% D2O
solution
Goddard
peak picking
Sparky
G. Marius Clore, Guillermo Bermejo, John Kuszewski, Charles D. Schwieters, and Nico Tjandra
refinement
Xplor-NIH
2.46
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
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 binding site.
none
1680
-62
5220
A
DC
4
A
N4
DC
4
1_555
A
HG
102
D
HG
HG
1_555
B
DT
25
B
N3
DT
11
1_555
178.4
A
DT
11
A
N3
DT
11
1_555
A
HG
101
C
HG
HG
1_555
B
DC
18
B
N4
DC
4
1_555
178.3
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')_minor
Concerted dynamics of metallo-base pairs in an A/B-form helical transition (minor species)
1
N
N
1
N
N
2
N
N
2
N
N
metalc
2.135
A
DC
4
A
N4
DC
4
1_555
A
HG
102
D
HG
HG
1_555
metalc
2.132
A
DT
11
A
N3
DT
11
1_555
A
HG
101
C
HG
HG
1_555
metalc
2.135
B
DC
18
B
N4
DC
4
1_555
A
HG
101
C
HG
HG
1_555
metalc
2.135
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
6FY7
PDB
1
1
6FY7
1
14
6FY7
1
14
6FY7
A
1
1
14
15
28
6FY7
15
28
6FY7
B
1
1
14
binding site for residue HG A 101
A
HG
101
Software
4
binding site for residue HG A 102
A
HG
102
Software
4
A
DA
10
A
DA
10
4
1_555
A
DT
11
A
DT
11
4
1_555
A
DA
12
A
DA
12
4
1_555
B
DC
18
B
DC
4
4
1_555
A
DC
4
A
DC
4
4
1_555
B
DA
24
B
DA
10
4
1_555
B
DT
25
B
DT
11
4
1_555
B
DA
26
B
DA
12
4
1_555