1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Nishizaki, T.
Iwai, S.
Ohkubo, T.
Kojima, C.
Nakamura, H.
Kyogoku, Y.
Ohtsuka, E.
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 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
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
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
US
Biochemistry
BICHAW
0033
0006-2960
35
4016
4025
10.1021/bi9519821
8672435
Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC).
1996
10.2210/pdb1dhh/pdb
pdb_00001dhh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA
2854.832
DNA/RNA (5'-D(*GP*G)-R(P*AP*GP*AP*U)-D(P*GP*AP*C)-3')
1
syn
polymer
CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA
2666.761
DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3')
1
syn
polymer
RIBONUCLEIC ACID
DEOXYRIBONUCLEIC ACID/RIBONUCLEIC ACID
DHD
DHD
no
no
(DG)(DG)AGAU(DG)(DA)(DC)
GGAGAUGAC
A
polydeoxyribonucleotide/polyribonucleotide hybrid
no
no
(DG)(DT)(DC)(DA)(DT)(DC)(DT)(DC)(DC)
GTCATCTCC
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-2.266
1
19
A
1
B
18
1.153
A_DG1:DC18_B
1
0.102
-0.530
-0.185
-0.306
-3.103
1
19
A
2
B
17
5.848
A_DG2:DC17_B
2
-4.593
-0.694
-0.076
-0.321
2.053
1
20
A
3
B
16
4.670
A_A3:DT16_B
3
-8.970
-0.342
0.180
-0.370
4.345
1
19
A
4
B
15
1.710
A_G4:DC15_B
4
-10.176
-0.225
0.086
-0.303
-3.696
1
20
A
5
B
14
-5.726
A_A5:DT14_B
5
-4.093
-0.412
0.115
-0.242
8.703
1
20
A
6
B
13
10.088
A_U6:DA13_B
6
-7.978
0.165
-0.193
-0.201
-7.184
1
19
A
7
B
12
0.778
A_DG7:DC12_B
7
-1.884
0.161
-0.290
-0.310
0.601
1
20
A
8
B
11
-0.505
A_DA8:DT11_B
8
-1.969
-0.433
0.018
-0.380
2.282
1
19
A
9
B
10
-1.240
A_DC9:DG10_B
9
-0.853
0.615
-0.044
-0.430
3.347
28.942
A
A
1
2
-0.678
B
B
18
17
3.332
-0.339
0.069
-1.396
AA_DG1DG2:DC17DC18_BB
1
-0.232
0.464
28.939
-2.716
-0.190
3.616
37.415
A
A
2
3
2.125
B
B
17
16
3.609
1.363
-0.855
0.146
AA_DG2A3:DT16DC17_BB
2
-0.188
0.293
37.390
0.030
1.305
3.357
37.354
A
A
3
4
27.227
B
B
16
15
3.424
16.843
-0.562
0.707
AA_A3G4:DC15DT16_BB
3
1.801
-2.911
33.415
-1.340
1.139
3.193
33.096
A
A
4
5
28.370
B
B
15
14
3.484
15.473
-1.226
-0.124
AA_G4A5:DT14DC15_BB
4
-5.761
10.562
28.785
-3.081
1.085
3.067
33.918
A
A
5
6
2.628
B
B
14
13
2.936
1.527
1.136
-0.056
AA_A5U6:DA13DT14_BB
5
5.184
-8.923
33.497
-0.322
-1.179
3.497
52.301
A
A
6
7
44.349
B
B
13
12
3.827
35.887
-0.446
0.949
AA_U6DG7:DC12DA13_BB
6
0.601
-0.743
38.689
-2.052
0.558
3.123
27.623
A
A
7
8
3.463
B
B
12
11
3.234
1.650
-0.319
-1.106
AA_DG7DA8:DT11DC12_BB
7
2.466
-5.174
27.467
-2.708
1.252
3.155
36.240
A
A
8
9
4.569
B
B
11
10
3.272
2.838
0.419
-1.099
AA_DA8DC9:DG10DT11_BB
8
-1.830
2.946
36.087
-2.159
-0.927
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1996-04-03
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
MINIMIZED AVERAGE STRUCTURE
Y
BNL
1995-10-18
REL
REL
A SUBSTRATE OF RNASE H
sample
A SUBSTRATE OF RNASE H
sample
1
100
mM
50
mM
3
mM
7.0
298
K
RMSD BOND DISTANCES 0.0077 ANGSTROMS RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE STRUCTURES WAS REFINED BY A COMBINATION OF RESTRAINED MOLECULAR DYNAMICS USING THE X-PLOR (V3.1F) PROGRAM (BRUNGER 1988) AND FULL RELAXATION MATRIX REFINEMENT OF THE TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRUM AT 150 MSEC.
MOLECULAR DYNAMICS, MATRIX RELAXATION
BRUNGER
refinement
X-PLOR
3.1F
G
1
n
1
DG
1
A
G
2
n
2
DG
2
A
A
3
n
3
A
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
U
6
n
6
U
6
A
G
7
n
7
DG
7
A
A
8
n
8
DA
8
A
C
9
n
9
DC
9
A
G
10
n
1
DG
10
B
T
11
n
2
DT
11
B
C
12
n
3
DC
12
B
A
13
n
4
DA
13
B
T
14
n
5
DT
14
B
C
15
n
6
DC
15
B
T
16
n
7
DT
16
B
C
17
n
8
DC
17
B
C
18
n
9
DC
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
A
3
0.052
SIDE CHAIN
1
A
U
6
0.057
SIDE CHAIN
1
4.06
0.30
108.30
112.36
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
4.39
0.50
113.10
117.49
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
DG
DG
DG
1
1
1
N
1
4.22
0.30
108.30
112.52
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.62
0.50
113.10
117.72
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.45
0.40
106.40
103.95
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
3.84
0.50
113.80
117.64
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
5.43
0.80
101.50
106.93
A
A
A
C3'
C2'
C1'
G
G
G
4
4
4
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
4
4
4
N
1
4.98
0.80
101.50
106.48
A
A
A
C3'
C2'
C1'
A
A
A
5
5
5
N
1
4.25
0.50
113.80
118.05
A
A
A
N7
C8
N9
A
A
A
5
5
5
N
1
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.76
0.50
113.10
117.86
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
1
-2.43
0.40
106.40
103.97
A
A
A
C8
N9
C4
DG
DG
DG
7
7
7
N
1
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
3.81
0.50
113.80
117.61
A
A
A
N7
C8
N9
DA
DA
DA
8
8
8
N
1
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
2.95
0.30
108.30
111.25
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
4.63
0.50
113.10
117.73
B
B
B
N7
C8
N9
DG
DG
DG
10
10
10
N
1
-2.58
0.40
106.40
103.82
B
B
B
C8
N9
C4
DG
DG
DG
10
10
10
N
1
3.33
0.30
108.30
111.63
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
2.52
0.30
108.30
110.82
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.30
0.30
108.30
110.60
B
B
B
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
3.76
0.50
113.80
117.56
B
B
B
N7
C8
N9
DA
DA
DA
13
13
13
N
1
2.36
0.30
108.30
110.66
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.79
0.30
108.30
111.09
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
2.59
0.30
108.30
110.89
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
2.65
0.30
108.30
110.95
B
B
B
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
4.29
0.30
108.30
112.59
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
18
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
18
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
18
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
17
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
17
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
17
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
B
DT
16
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
B
DT
16
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
B
DC
15
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
B
DC
15
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
B
DC
15
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
A
5
A
N1
A
5
1_555
B
DT
14
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
A
5
A
N6
A
5
1_555
B
DT
14
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
U
6
A
N3
U
6
1_555
B
DA
13
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
U
6
A
O4
U
6
1_555
B
DA
13
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
12
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
12
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
12
B
N4
DC
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-RNA HYBRID
DNA/RNA HYBRID IN DNA DUPLEX, DNA-RNA HYBRID
1DHH
PDB
1
1DHH
1DHH
PDB
2
1DHH
1
9
1DHH
1
9
1DHH
A
1
1
9
10
18
1DHH
10
18
1DHH
B
2
1
9
1
P 1