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.
Ohtsuka, E.
Nakamura, H.
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 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
C10 H16 N3 O8 P
337.223
n
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
RNA linking
C11 H16 N5 O8 P
377.247
n
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H15 N2 O9 P
338.208
n
O2'-METHYLURIDINE 5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
US
Biochemistry
BICHAW
0033
0006-2960
36
2577
2585
10.1021/bi962297c
9054564
Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center.
1997
10.2210/pdb1nao/pdb
pdb_00001nao
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
A SUBSTRATE OF RNASE H
2934.831
RNA (5'-R(*GP*GP*AP*GP*AP*UP*GP*AP*C)-3')
1
syn
polymer
A SUBSTRATE OF RNASE H
2802.865
DNA/RNA (5'-R(*OMGP*OMUP*OMC)-D(P*AP*TP*CP*T)-R(P*OMCP*OMC)-3')
1
syn
polymer
no
no
GGAGAUGAC
GGAGAUGAC
A
polyribonucleotide
no
yes
(OMG)(OMU)(OMC)(DA)(DT)(DC)(DT)(OMC)(OMC)
GUCATCTCC
B
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-2.528
1
19
A
1
B
18
0.259
A_G1:OMC18_B
1
0.759
-0.633
-0.094
-0.327
-1.293
1
19
A
2
B
17
2.598
A_G2:OMC17_B
2
-12.662
-0.895
0.036
-0.376
0.589
1
20
A
3
B
16
-3.118
A_A3:DT16_B
3
0.971
-0.219
-0.326
-0.212
2.800
1
19
A
4
B
15
-0.586
A_G4:DC15_B
4
-5.671
-0.360
0.149
-0.267
-5.205
1
20
A
5
B
14
-3.545
A_A5:DT14_B
5
-5.529
0.057
-0.170
-0.123
8.351
1
20
A
6
B
13
-0.610
A_U6:DA13_B
6
-6.664
0.581
-0.225
-0.276
-6.473
1
19
A
7
B
12
6.064
A_G7:OMC12_B
7
-8.654
-1.023
-0.543
-0.395
2.847
1
20
A
8
B
11
-14.621
A_A8:OMU11_B
8
-4.469
1.480
-0.061
-0.158
6.487
1
19
A
9
B
10
2.063
A_C9:OMG10_B
9
0.254
0.684
-0.274
-0.140
3.687
41.487
A
A
1
2
-4.571
B
B
18
17
3.528
-3.227
-1.260
-0.522
AA_G1G2:OMC17OMC18_BB
1
-5.407
7.660
41.028
-0.356
1.141
3.752
41.262
A
A
2
3
-23.597
B
B
17
16
4.061
-16.207
-1.237
0.190
AA_G2A3:DT16OMC17_BB
2
-2.496
3.634
37.995
2.449
1.419
3.925
30.406
A
A
3
4
18.620
B
B
16
15
4.092
9.606
0.470
0.080
AA_A3G4:DC15DT16_BB
3
0.615
-1.191
28.877
-2.271
-0.740
3.406
43.590
A
A
4
5
33.810
B
B
15
14
3.812
23.815
-1.454
0.118
AA_G4A5:DT14DC15_BB
4
-3.769
5.352
36.588
-2.620
1.519
2.911
27.049
A
A
5
6
-3.806
B
B
14
13
2.851
-1.778
0.753
-1.575
AA_A5U6:DA13DT14_BB
5
-1.179
2.523
26.967
-2.969
-1.874
1.906
36.366
A
A
6
7
34.320
B
B
13
12
3.473
20.254
0.815
-1.759
AA_U6G7:OMC12DA13_BB
6
-2.073
3.512
30.293
-5.370
-1.568
3.132
44.543
A
A
7
8
3.869
B
B
12
11
3.018
2.929
-2.589
-0.567
AA_G7A8:OMU11OMC12_BB
7
-2.905
3.838
44.361
-1.002
3.164
3.717
28.593
A
A
8
9
-7.517
B
B
11
10
3.219
-3.693
2.319
-2.049
AA_A8C9:OMG10OMU11_BB
8
3.660
-7.450
28.126
-3.252
-3.808
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1997-01-27
1
1
2008-03-10
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
Y
BNL
1996-03-29
REL
REL
00MM NACL, 50MM NA PHOSPHATE, 3MM EDTA
AVERAGED
10
1
7.0
313
K
simulated annealing
BRUNGER
refinement
X-PLOR 3.1F
3.1F
structure solution
X-PLOR
600
Bruker
AMX600
G
1
n
1
G
1
A
G
2
n
2
G
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
G
7
A
A
8
n
8
A
8
A
C
9
n
9
C
9
A
OMG
10
n
1
OMG
10
B
OMU
11
n
2
OMU
11
B
OMC
12
n
3
OMC
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
OMC
17
n
8
OMC
17
B
OMC
18
n
9
OMC
18
B
author_defined_assembly
2
dimeric
B
OMG
10
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
B
OMG
1
G
B
OMU
11
O2'-METHYLURIDINE 5'-MONOPHOSPHATE
B
OMU
2
U
B
OMC
12
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
3
C
B
OMC
17
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
8
C
B
OMC
18
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
9
C
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
5.17
0.80
101.50
106.67
A
A
A
C3'
C2'
C1'
G
G
G
1
1
1
N
1
4.37
0.50
113.10
117.47
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
3.82
0.50
113.80
117.62
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
4
4
4
N
1
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
4
4
4
N
1
4.25
0.50
113.80
118.05
A
A
A
N7
C8
N9
A
A
A
5
5
5
N
1
5.28
0.80
101.50
106.78
A
A
A
C3'
C2'
C1'
U
U
U
6
6
6
N
1
4.93
0.70
108.50
113.43
A
A
A
O4'
C1'
N1
U
U
U
6
6
6
N
1
4.94
0.80
101.50
106.44
A
A
A
C3'
C2'
C1'
G
G
G
7
7
7
N
1
4.43
0.50
113.10
117.53
A
A
A
N7
C8
N9
G
G
G
7
7
7
N
1
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
8
8
8
N
1
2.51
0.30
108.30
110.81
B
B
B
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
4.05
0.50
113.80
117.85
B
B
B
N7
C8
N9
DA
DA
DA
13
13
13
N
1
3.31
0.30
108.30
111.61
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
3.40
0.30
108.30
111.70
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.16
0.30
108.30
111.46
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION STRUCTURE OF AN RNA 2'-O-METHYLATED RNA DUPLEX CONTAINING AN RNA/DNA HYBRID SEGMENT AT THE CENTER, NMR, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.618
both
B
OMG
10
B
O3'
OMG
1
1_555
B
OMU
11
B
P
OMU
2
1_555
covale
1.609
both
B
OMU
11
B
O3'
OMU
2
1_555
B
OMC
12
B
P
OMC
3
1_555
covale
1.617
both
B
OMC
12
B
O3'
OMC
3
1_555
B
DA
13
B
P
DA
4
1_555
covale
1.621
both
B
DT
16
B
O3'
DT
7
1_555
B
OMC
17
B
P
OMC
8
1_555
covale
1.615
both
B
OMC
17
B
O3'
OMC
8
1_555
B
OMC
18
B
P
OMC
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
OMC
18
B
N3
OMC
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
OMC
18
B
O2
OMC
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
OMC
18
B
N4
OMC
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
OMC
17
B
N3
OMC
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
OMC
17
B
O2
OMC
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
OMC
17
B
N4
OMC
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
G
7
A
N1
G
7
1_555
B
OMC
12
B
N3
OMC
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
OMC
12
B
O2
OMC
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
OMC
12
B
N4
OMC
3
1_555
hydrog
WATSON-CRICK
A
A
8
A
N1
A
8
1_555
B
OMU
11
B
N3
OMU
2
1_555
hydrog
WATSON-CRICK
A
A
8
A
N6
A
8
1_555
B
OMU
11
B
O4
OMU
2
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
OMG
10
B
N1
OMG
1
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
OMG
10
B
O6
OMG
1
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
OMG
10
B
N2
OMG
1
1_555
DNA-RNA HYBRID
DNA/RNA DUPLEX, DNA-RNA HYBRID
1NAO
PDB
1
1NAO
1NAO
PDB
2
1NAO
1
9
1NAO
1
9
1NAO
A
1
1
9
10
18
1NAO
10
18
1NAO
B
2
1
9
1
P 1