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
C9 H13 N2 O8 P
308.182
1-[2-DEOXY-RIBOFURANOSYL]-1H-[3-NITRO-PYRROL]-5'-PHOSPHATE
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/pdb1dk6/pdb
pdb_00001dk6
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
2716.784
5'-D(GP*TP*AP*CP*(NP3)P*CP*AP*TP*GP*)-3'
1
syn
polymer
no
no
(DC)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DC)
CATGAGTAC
A
polydeoxyribonucleotide
no
yes
(DG)(DT)(DA)(DC)(NP3)(DC)(DA)(DT)(DG)
GTACNCATG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-7.626
1
19
A
1
B
18
-3.915
A_DC1:DG18_B
1
15.615
0.246
0.324
-0.441
9.979
1
20
A
2
B
17
-2.394
A_DA2:DT17_B
2
-1.206
-0.308
0.505
-0.228
6.059
1
20
A
3
B
16
-0.612
A_DT3:DA16_B
3
-6.086
-0.058
0.104
-0.388
-5.286
1
19
A
4
B
15
1.715
A_DG4:DC15_B
4
-15.324
-0.389
-0.356
-0.520
7.519
1
19
A
6
B
13
6.230
A_DG6:DC13_B
5
-4.396
-0.934
0.548
-0.337
5.839
1
20
A
7
B
12
2.046
A_DT7:DA12_B
6
-13.062
-0.201
0.078
-0.341
-10.103
1
20
A
8
B
11
7.281
A_DA8:DT11_B
7
-13.704
-0.018
0.065
-0.271
-28.912
1
19
A
9
B
10
5.372
A_DC9:DG10_B
8
9.510
0.418
1.243
-0.459
1.887
30.441
A
A
1
2
37.542
B
B
18
17
2.648
18.400
0.304
-0.368
AA_DC1DA2:DT17DG18_BB
1
-1.692
3.452
24.298
-3.556
-0.842
3.254
37.567
A
A
2
3
-0.460
B
B
17
16
3.252
-0.296
0.122
-0.695
AA_DA2DT3:DA16DT17_BB
2
3.792
-5.898
37.381
-1.040
0.303
2.887
35.633
A
A
3
4
15.482
B
B
16
15
3.224
9.356
-0.203
-0.778
AA_DT3DG4:DC15DA16_BB
3
3.375
-5.585
34.260
-2.568
0.799
5.188
71.733
A
A
4
6
10.190
B
B
15
13
5.428
11.896
0.517
-1.083
AA_DG4DG6:DC13DC15_BB
4
-3.590
3.075
70.792
-1.581
-0.640
2.898
31.746
A
A
6
7
1.127
B
B
13
12
3.028
0.615
-1.029
-0.995
AA_DG6DT7:DA12DC13_BB
5
3.076
-5.633
31.594
-1.921
2.394
2.996
40.512
A
A
7
8
12.746
B
B
12
11
3.228
8.757
0.270
-0.831
AA_DT7DA8:DT11DA12_BB
6
2.485
-3.617
39.518
-2.144
-0.122
3.685
34.557
A
A
8
9
-4.710
B
B
11
10
3.813
-2.768
0.282
-0.813
AA_DA8DC9:DG10DT11_BB
7
-8.563
14.574
33.399
-0.869
-2.020
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-01-11
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
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
285
K
THE STRUCTURE IS BASED ON A TOTAL OF 624 RESTRAINTS, 198 ARE DERIVED FROM
ASSIGNED NOES, 394 ARE LOWER BOUND NOE-DERIVED RESTRAINTS TO UNASSIGN 1H5*/2H5*
PROTONS, AND 32 ARE DIHEDRAL ANGLE RESTRAINTS
SIMULATED ANNEALING MOLECULAR DYNAMICS
4.5MM DUPLEX; 100MM NACL, 10MM NAOP, 1MM EDTA, PH 7
LIU
structure solution
CORMA
5.2
BORGIAS, JAMES
iterative matrix relaxation
MARDIGRAS
5.2
DELAGLIO
processing
NMRPipe
1.7
BRUNGER
refinement
X-PLOR
V3.840
VARIAN
collection
VNMR
6.1B
DAY, KNELLER
data analysis
Sparky
3.74
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
NP3
14
n
5
NP3
14
B
CYT
15
n
6
DC
15
B
ADE
16
n
7
DA
16
B
THY
17
n
8
DT
17
B
G
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
H41
O6
DC
DG
1
18
1.47
1
A
B
H21
O2
DG
DC
4
15
1.50
1
A
B
O2
H21
DC
DG
9
10
1.52
1
A
B
O6
H41
DG
DC
4
15
1.52
1
A
B
H21
O2
DG
DC
6
13
1.54
1
A
B
H1
N3
DG
DC
4
15
1.58
1
A
B
H3
N1
DT
DA
7
12
1.59
1
A
B
H3
N1
DT
DA
3
16
1.59
1
A
DG
4
0.088
SIDE CHAIN
1
A
DG
6
0.080
SIDE CHAIN
1
B
DG
10
0.104
SIDE CHAIN
1
B
DC
13
0.111
SIDE CHAIN
1
B
DA
16
0.119
SIDE CHAIN
1
B
DT
17
0.079
SIDE CHAIN
1
B
DG
18
0.080
SIDE CHAIN
1
-4.85
0.80
105.90
101.05
A
A
A
O4'
C1'
C2'
DA
DA
DA
2
2
2
N
1
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
1
3.06
0.50
113.80
116.86
A
A
A
N7
C8
N9
DA
DA
DA
2
2
2
N
1
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
3.57
0.50
113.10
116.67
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
3.08
0.50
113.80
116.88
A
A
A
N7
C8
N9
DA
DA
DA
5
5
5
N
1
3.60
0.50
113.10
116.70
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
1
3.38
0.50
113.80
117.18
A
A
A
N7
C8
N9
DA
DA
DA
8
8
8
N
1
7.13
0.30
108.30
115.43
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.40
0.50
113.10
116.50
B
B
B
N7
C8
N9
DG
DG
DG
10
10
10
N
1
-2.42
0.40
106.40
103.98
B
B
B
C8
N9
C4
DG
DG
DG
10
10
10
N
1
7.21
1.10
109.80
117.01
B
B
B
C5'
C4'
O4'
DA
DA
DA
12
12
12
N
1
5.04
0.30
108.30
113.34
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
6.65
1.10
109.80
116.45
B
B
B
C5'
C4'
O4'
DC
DC
DC
15
15
15
N
1
4.44
0.30
108.30
112.74
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
-4.89
0.80
105.90
101.01
B
B
B
O4'
C1'
C2'
DA
DA
DA
16
16
16
N
1
3.40
0.50
113.80
117.20
B
B
B
N7
C8
N9
DA
DA
DA
16
16
16
N
1
4.14
0.60
119.00
123.14
B
B
B
C4
C5
C7
DT
DT
DT
17
17
17
N
1
-6.35
0.60
122.90
116.55
B
B
B
C6
C5
C7
DT
DT
DT
17
17
17
N
1
2.15
0.30
108.30
110.45
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
3.72
0.50
113.10
116.82
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
A
A
C5
C7
DT
DT
3
3
0.037
0.006
1.496
1.533
N
1
B
B
C5
C7
DT
DT
11
11
0.036
0.006
1.496
1.532
N
NMR structure analysis of the DNA nine base pair duplex D(CATGAGTAC) D(GTAC(NP3)CATG)
1
N
N
2
N
N
covale
1.624
both
B
DC
13
B
O3'
DC
4
1_555
B
NP3
14
B
P
NP3
5
1_555
covale
1.621
both
B
NP3
14
B
O3'
NP3
5
1_555
B
DC
15
B
P
DC
6
1_555
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
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 DOUBLE HELIX, 3-NITROPYRROLE, DNA
1DK6
PDB
1
1DK6
1DK6
PDB
2
1DK6
1
9
1DK6
1
9
1DK6
A
1
1
9
10
18
1DK6
10
18
1DK6
B
2
1
9
1
P 1