0.018587
0.000000
0.006729
0.000000
0.051546
0.000000
0.000000
0.000000
0.021211
0.00000
0.00000
0.00000
THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED (NAMED RHD), TWO WITH FULL OCCUPANCY FACTORS (RESIDUES 19 AND 20) AND TWO WITH PARTIAL OCCUPANCIES (RESIDUES 21 AND 22).
Cruse, W.
Saludjian, P.
Biala, E.
Strazewski, P.
Prange, T.
Kennard, O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
109.90
90.00
53.800
19.400
50.140
C9 H12 Br N2 O8 P
387.078
n
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
H18 N6 Rh 3
205.089
RHODIUM HEXAMINE ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
O
N
9
N
BR
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
O
N
35
N
P
N
36
N
O
N
37
N
O
N
38
N
O
N
39
N
C
N
40
R
C
N
41
N
O
N
42
S
C
N
43
N
O
N
44
R
C
N
45
N
O
N
46
R
C
N
47
N
N
N
48
N
C
N
49
N
O
N
50
N
N
N
51
N
C
N
52
N
N
N
53
N
C
N
54
N
C
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
O
N
70
N
P
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
C
N
75
R
C
N
76
N
O
N
77
S
C
N
78
N
O
N
79
R
C
N
80
N
O
N
81
R
C
Y
82
N
N
Y
83
N
C
Y
84
N
N
Y
85
N
C
N
86
N
C
N
87
N
O
N
88
N
N
N
89
N
C
N
90
N
N
N
91
N
N
Y
92
N
C
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
O
N
108
N
H
N
109
N
H
N
110
N
RH
N
111
N
N
N
112
N
N
N
113
N
N
N
114
N
N
N
115
N
N
N
116
N
N
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
O
N
136
N
P
N
137
N
O
N
138
N
O
N
139
N
O
N
140
N
C
N
141
R
C
N
142
N
O
N
143
S
C
N
144
N
O
N
145
R
C
N
146
N
O
N
147
R
C
N
148
N
N
N
149
N
C
N
150
N
O
N
151
N
N
N
152
N
C
N
153
N
O
N
154
N
C
N
155
N
C
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
N
10
N
doub
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
Y
95
N
sing
Y
96
N
sing
Y
97
N
doub
N
98
N
sing
Y
99
N
sing
N
100
N
sing
Y
101
N
doub
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
91
4160
4164
10.1073/pnas.91.10.4160
7514296
Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.
1994
10.2210/pdb165d/pdb
pdb_0000165d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
1
IMAGE PLATE
MARRESEARCH
DIFFRACTOMETER
ENRAF-NONIUS FAST
M
x-ray
1
M
x-ray
2
1.0
1.0
LURE
SYNCHROTRON
LURE
2887.600
DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')
2
syn
polymer
205.089
RHODIUM HEXAMINE ION
4
syn
non-polymer
18.015
water
54
nat
water
no
yes
GCUUCGGC(BRU)
GCUUCGGCU
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
2.13
42.26
VAPOR DIFFUSION, SITTING DROP
6.30
pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
277.00
WATER
1
LI CACODYLATE
1
[RH(NH3)6]CL3
1
0.915
1
19
A
1
B
17
1.089
A_G1:C17_B
1
-13.439
-0.507
-0.271
-0.379
5.509
1
19
A
2
B
16
1.106
A_C2:G16_B
2
-11.964
0.162
-0.027
-0.263
4.776
28
A
3
B
15
-1.858
A_U3:G15_B
3
-10.255
2.233
-0.124
-0.490
2.026
A
4
B
14
-40.981
A_U4:C14_B
4
2.784
-0.638
0.220
0.206
7.013
A
5
B
13
-39.828
A_C5:U13_B
5
-3.734
0.733
-0.397
0.119
-0.232
1
28
A
6
B
12
-1.239
A_G6:U12_B
6
-12.882
-2.244
-0.180
-0.601
-4.817
1
19
A
7
B
11
1.012
A_G7:C11_B
7
-12.774
-0.178
-0.160
-0.118
-3.779
1
19
A
8
B
10
-0.871
A_C8:G10_B
8
-6.718
0.445
0.090
-0.195
3.012
35.993
A
A
1
2
7.535
B
B
17
16
3.238
4.640
-0.228
-1.669
AA_G1C2:G16C17_BB
1
-2.718
4.415
35.602
-3.335
-0.002
3.163
38.323
A
A
2
3
8.177
B
B
16
15
3.377
5.349
-0.023
-1.320
AA_C2U3:G15G16_BB
2
2.142
-3.275
37.904
-2.684
0.305
3.479
22.320
A
A
3
4
17.641
B
B
15
14
3.406
6.663
-3.926
-1.958
AA_U3U4:C14G15_BB
3
-5.163
13.668
20.686
-7.783
8.032
3.164
39.169
A
A
4
5
9.174
B
B
14
13
3.489
6.124
0.004
-1.867
AA_U4C5:U13C14_BB
4
2.016
-3.019
38.655
-3.536
0.241
2.344
27.932
A
A
5
6
25.709
B
B
13
12
3.434
12.018
3.202
-1.635
AA_C5G6:U12U13_BB
5
-0.651
1.393
25.252
-6.047
-6.779
3.103
40.218
A
A
6
7
11.075
B
B
12
11
3.456
7.573
0.186
-1.616
AA_G6G7:C11U12_BB
6
-0.690
1.009
39.522
-3.219
-0.350
3.497
35.346
A
A
7
8
-1.251
B
B
11
10
3.462
-0.759
0.107
-1.732
AA_G7C8:G10C11_BB
7
-0.073
0.121
35.338
-2.734
-0.187
diffrn_detector
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_special_symmetry
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Data collection
Database references
Derived calculations
1
0
1994-08-31
1
1
2008-05-22
1
2
2011-07-13
1
3
2018-04-18
1
4
2024-02-07
_diffrn_detector.detector
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1994-03-21
REL
RHD
RHODIUM HEXAMINE ION
HOH
water
RHD
19
2
RHD
RHD
19
A
RHD
20
2
RHD
RHD
20
A
RHD
22
2
RHD
RHD
22
A
RHD
21
2
RHD
RHD
21
B
HOH
23
3
HOH
HOH
23
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
33
3
HOH
HOH
33
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
41
3
HOH
HOH
41
A
HOH
43
3
HOH
HOH
43
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
A
HOH
51
3
HOH
HOH
51
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
59
3
HOH
HOH
59
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
66
3
HOH
HOH
66
A
HOH
73
3
HOH
HOH
73
A
HOH
74
3
HOH
HOH
74
A
HOH
24
3
HOH
HOH
24
B
HOH
32
3
HOH
HOH
32
B
HOH
34
3
HOH
HOH
34
B
HOH
39
3
HOH
HOH
39
B
HOH
40
3
HOH
HOH
40
B
HOH
42
3
HOH
HOH
42
B
HOH
44
3
HOH
HOH
44
B
HOH
45
3
HOH
HOH
45
B
HOH
46
3
HOH
HOH
46
B
HOH
49
3
HOH
HOH
49
B
HOH
50
3
HOH
HOH
50
B
HOH
52
3
HOH
HOH
52
B
HOH
55
3
HOH
HOH
55
B
HOH
58
3
HOH
HOH
58
B
HOH
62
3
HOH
HOH
62
B
HOH
67
3
HOH
HOH
67
B
HOH
68
3
HOH
HOH
68
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
HOH
75
3
HOH
HOH
75
B
HOH
76
3
HOH
HOH
76
B
G
1
n
1
G
1
A
C
2
n
2
C
2
A
U
3
n
3
U
3
A
U
4
n
4
U
4
A
C
5
n
5
C
5
A
G
6
n
6
G
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
+U
9
n
9
BRU
9
A
G
10
n
1
G
10
B
C
11
n
2
C
11
B
U
12
n
3
U
12
B
U
13
n
4
U
13
B
C
14
n
5
C
14
B
G
15
n
6
G
15
B
G
16
n
7
G
16
B
C
17
n
8
C
17
B
+U
18
n
9
BRU
18
B
author_defined_assembly
2
dimeric
A
BRU
9
A
BRU
9
DU
B
BRU
18
B
BRU
9
DU
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
B
BRU
18
B
BRU
9
1
A
A
O
O
HOH
HOH
51
61
1.43
1
B
B
O
O
HOH
HOH
50
71
2.05
1
A
G
1
0.075
SIDE CHAIN
1
A
G
7
0.073
SIDE CHAIN
1
B
C
11
0.072
SIDE CHAIN
1
-4.37
0.70
122.20
117.83
A
A
A
N3
C2
O2
U
U
U
3
3
3
N
1
7.03
1.10
110.50
117.53
A
A
A
O3'
P
OP2
U
U
U
3
4
4
Y
1
5.02
0.70
108.50
113.52
B
B
B
O4'
C1'
N1
U
U
U
13
13
13
N
1
-11.63
1.90
104.00
92.37
B
B
B
O3'
P
O5'
C
G
G
14
15
15
Y
1
18.09
1.10
110.50
128.59
B
B
B
O3'
P
OP2
C
G
G
14
15
15
Y
1
6.74
1.10
110.50
117.24
B
B
B
O3'
P
OP2
G
G
G
15
16
16
Y
1
13.40
1.10
110.50
123.90
B
B
B
O3'
P
OP2
C
BRU
BRU
17
18
18
A
A
Y
1
-28.72
2.20
105.20
76.48
B
B
B
O3'
P
OP2
C
BRU
BRU
17
18
18
B
B
Y
1
16.67
1.10
110.50
127.17
B
B
B
O3'
P
OP1
C
BRU
BRU
17
18
18
B
B
Y
0.18
0.18
1.550
10.000
6098
1
2.000
1.550
10.000
54
474
31
389
0
0.017
0.030
2.10
1.600
165D
6093
2.000
1,2
refinement
X-PLOR
THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
covale
1.584
both
A
C
8
A
O3'
C
8
1_555
A
BRU
9
A
P
BRU
9
1_555
covale
1.617
both
A
B
C
17
B
O3'
C
8
1_555
B
BRU
18
B
P
BRU
9
1_555
covale
1.632
both
B
B
C
17
B
O3'
C
8
1_555
B
BRU
18
B
P
BRU
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
17
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
17
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
17
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
G
16
B
N1
G
7
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
G
16
B
O6
G
7
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
G
16
B
N2
G
7
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
N3
U
3
1_555
B
G
15
B
O6
G
6
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
O2
U
3
1_555
B
G
15
B
N1
G
6
1_555
hydrog
U-C MISPAIR
A
U
4
A
O4
U
4
1_555
B
C
14
B
N4
C
5
1_555
hydrog
C-U MISPAIR
A
C
5
A
N4
C
5
1_555
B
U
13
B
O4
U
4
1_555
hydrog
TYPE_28_PAIR
A
G
6
A
N1
G
6
1_555
B
U
12
B
O2
U
3
1_555
hydrog
TYPE_28_PAIR
A
G
6
A
O6
G
6
1_555
B
U
12
B
N3
U
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
B
C
11
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
C
11
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
C
11
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
10
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
10
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
10
B
N2
G
1
1_555
DNA-RNA HYBRID
A-DNA/RNA, DOUBLE HELIX, OVERHANGING BASES, MODIFIED, MISMATCHED, DNA-RNA HYBRID
165D
PDB
1
165D
1
9
165D
1
9
165D
A
1
1
9
10
18
165D
10
18
165D
B
1
1
9
BINDING SITE FOR RESIDUE RHD A 19
A
RHD
19
Software
5
BINDING SITE FOR RESIDUE RHD A 20
A
RHD
20
Software
5
BINDING SITE FOR RESIDUE RHD B 21
B
RHD
21
Software
5
BINDING SITE FOR RESIDUE RHD A 22
A
RHD
22
Software
6
A
C
5
A
C
5
5
1_555
A
G
6
A
G
6
5
1_555
A
G
7
A
G
7
5
1_555
A
HOH
26
G
HOH
5
1_555
B
HOH
72
H
HOH
5
1_555
A
C
5
A
C
5
5
4_546
A
G
7
A
G
7
5
1_545
A
C
8
A
C
8
5
1_545
B
C
14
B
C
5
5
4_546
B
HOH
45
H
HOH
5
4_546
A
U
3
A
U
3
5
1_555
B
G
15
B
G
6
5
1_555
B
G
16
B
G
7
5
1_555
B
HOH
34
H
HOH
5
1_555
B
HOH
46
H
HOH
5
1_555
A
C
2
A
C
2
6
2_566
A
U
3
A
U
3
6
2_566
A
BRU
9
A
BRU
9
6
1_555
B
C
11
B
C
2
6
2_556
B
U
12
B
U
3
6
2_556
B
HOH
32
H
HOH
6
2_556
5
C 1 2 1