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6
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6
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7
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7
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8
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8
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8
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8
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8
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8
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8
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8
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8
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9
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9
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9
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9
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9
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9
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9
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9
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O
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9
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9
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9
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9
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9
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1
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1
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1
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1
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1
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1
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O
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1
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1
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1
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1
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1
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1
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1
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O
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1
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1
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1
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1
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1
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2
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2
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2
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2
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2
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2
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2
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2
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2
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O
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2
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2
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2
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2
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2
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O
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2
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0.41
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2
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0.43
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2
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O
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2
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2
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2
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3
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3
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3
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3
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3
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3
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3
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O
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3
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7.286
9.297
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3
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O
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3
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3
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3
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3.919
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3
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3
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O
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3
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4.572
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12
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3
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4.236
1.554
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12
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N4
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N
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O
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N1
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N1
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1.000000
0.000000
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1.000000
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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
C9 H14 N3 O8 P
323.197
y
CYTIDINE-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/pdb1drn/pdb
pdb_00001drn
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
2854.833
DNA/RNA (5'-D(*GP*GP*AP*GP*A)-R(P*UP*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
DDH
DDH
no
no
(DG)(DG)(DA)(DG)(DA)UGAC
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
-0.669
1
19
A
1
B
18
-1.966
A_DG1:DC18_B
1
-3.214
-0.475
0.079
-0.391
-0.117
1
19
A
2
B
17
3.674
A_DG2:DC17_B
2
0.604
-0.476
-0.101
-0.057
-0.582
1
20
A
3
B
16
6.094
A_DA3:DT16_B
3
-2.994
-0.748
-0.035
-0.438
-0.065
1
19
A
4
B
15
2.647
A_DG4:DC15_B
4
-2.404
-1.038
0.034
-0.398
-1.605
1
20
A
5
B
14
5.445
A_DA5:DT14_B
5
-4.396
-0.580
-0.021
-0.345
1.851
1
20
A
6
B
13
0.436
A_U6:DA13_B
6
-1.525
0.465
-0.109
-0.343
-1.969
1
19
A
7
B
12
7.669
A_G7:DC12_B
7
-4.804
-1.334
0.015
-0.452
0.235
1
20
A
8
B
11
-0.771
A_A8:DT11_B
8
-5.307
-0.436
0.063
-0.381
4.268
1
19
A
9
B
10
4.174
A_C9:DG10_B
9
-3.614
1.405
-0.142
-0.496
3.279
33.648
A
A
1
2
21.508
B
B
18
17
3.488
12.168
0.557
0.212
AA_DG1DG2:DC17DC18_BB
1
-2.911
5.145
31.298
-1.767
-1.473
2.730
30.363
A
A
2
3
10.278
B
B
17
16
3.086
5.341
-0.057
-1.689
AA_DG2DA3:DT16DC17_BB
2
-4.059
7.811
29.630
-4.192
-0.625
4.025
29.528
A
A
3
4
-11.501
B
B
16
15
3.930
-5.825
0.180
-0.896
AA_DA3DG4:DC15DT16_BB
3
-0.617
1.217
28.954
-0.236
-0.515
3.043
34.429
A
A
4
5
8.671
B
B
15
14
3.193
5.114
-0.143
-0.820
AA_DG4DA5:DT14DC15_BB
4
-0.368
0.623
34.056
-2.149
0.186
3.077
35.507
A
A
5
6
2.334
B
B
14
13
3.118
1.423
0.425
-0.963
AA_DA5U6:DA13DT14_BB
5
-0.126
0.207
35.479
-1.777
-0.714
2.778
23.905
A
A
6
7
8.018
B
B
13
12
3.046
3.294
0.140
-1.241
AA_U6G7:DC12DA13_BB
6
-4.189
10.197
23.312
-3.964
-1.567
3.443
44.906
A
A
7
8
4.117
B
B
12
11
3.388
3.141
-0.980
0.221
AA_G7A8:DT11DC12_BB
7
-2.570
3.369
44.732
-0.008
1.039
3.620
40.561
A
A
8
9
-0.317
B
B
11
10
3.577
-0.220
0.688
-0.701
AA_A8C9:DG10DT11_BB
8
2.953
-4.264
40.457
-0.985
-0.631
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
1995-11-15
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
DA
3
A
G
4
n
4
DG
4
A
A
5
n
5
DA
5
A
U
6
n
6
U
6
A
G
7
n
7
G
7
A
A
8
n
8
A
8
A
C
9
n
9
C
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
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
DG
DG
DG
1
1
1
N
1
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.38
0.50
113.10
117.48
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
3.13
0.30
108.30
111.43
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
4.04
0.50
113.80
117.84
A
A
A
N7
C8
N9
DA
DA
DA
3
3
3
N
1
3.22
0.30
108.30
111.52
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.62
0.50
113.10
117.72
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.48
0.40
106.40
103.92
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
4.00
0.50
113.80
117.80
A
A
A
N7
C8
N9
DA
DA
DA
5
5
5
N
1
5.24
0.80
101.50
106.74
A
A
A
C3'
C2'
C1'
G
G
G
7
7
7
N
1
4.53
0.70
108.50
113.03
A
A
A
O4'
C1'
N9
G
G
G
7
7
7
N
1
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
1
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
G
G
G
7
7
7
N
1
3.90
0.50
113.80
117.70
A
A
A
N7
C8
N9
A
A
A
8
8
8
N
1
2.82
0.30
108.30
111.12
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
4.70
0.50
113.10
117.80
B
B
B
N7
C8
N9
DG
DG
DG
10
10
10
N
1
-2.59
0.40
106.40
103.81
B
B
B
C8
N9
C4
DG
DG
DG
10
10
10
N
1
2.96
0.30
108.30
111.26
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
2.22
0.30
108.30
110.52
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
3.63
0.30
108.30
111.93
B
B
B
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
3.80
0.50
113.80
117.60
B
B
B
N7
C8
N9
DA
DA
DA
13
13
13
N
1
-3.68
0.60
122.90
119.22
B
B
B
C6
C5
C7
DT
DT
DT
14
14
14
N
1
2.90
0.30
108.30
111.20
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
2.28
0.30
108.30
110.58
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
2.80
0.30
108.30
111.10
B
B
B
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
2.42
0.30
108.30
110.72
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(GGAGA)R(UGAC)/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
DA
3
A
N1
DA
3
1_555
B
DT
16
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
16
B
O4
DT
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
DA
5
A
N1
DA
5
1_555
B
DT
14
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
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
G
7
A
N1
G
7
1_555
B
DC
12
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
DC
12
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
DC
12
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
A
8
A
N1
A
8
1_555
B
DT
11
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
A
8
A
N6
A
8
1_555
B
DT
11
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
DG
10
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
DG
10
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
DG
10
B
N2
DG
1
1_555
DNA-RNA HYBRID
DOUBLE HELIX, DNA/RNA HYBRID, DNA-RNA HYBRID
1DRN
PDB
1
1DRN
1DRN
PDB
2
1DRN
1
9
1DRN
1
9
1DRN
A
1
1
9
10
18
1DRN
10
18
1DRN
B
2
1
9
1
P 1