0.018580
0.000000
0.006726
0.000000
0.051600
0.000000
0.000000
0.000000
0.021143
0.000000
0.000000
0.000000
Cruse, W.
Saludjian, P.
Neuman, A.
Prange, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
109.90
90.00
53.820
19.380
50.300
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
Cl -1
35.453
CHLORIDE ION
non-polymer
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
C9 H12 Cl N2 O8 P
342.627
n
5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
DNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
N
N
20
N
C
N
21
N
C
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
H
N
35
N
H
N
36
N
CL
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
R
C
N
48
N
O
N
49
R
C
Y
50
N
N
Y
51
N
C
Y
52
N
N
Y
53
N
C
N
54
N
C
N
55
N
O
N
56
N
N
N
57
N
C
N
58
N
N
N
59
N
N
Y
60
N
C
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
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
O
N
76
N
H
N
77
N
H
N
78
N
RH
N
79
N
N
N
80
N
N
N
81
N
N
N
82
N
N
N
83
N
N
N
84
N
N
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
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
O
N
104
N
P
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
C
N
109
R
C
N
110
N
O
N
111
S
C
N
112
N
O
N
113
R
C
N
114
N
O
N
115
R
C
N
116
N
N
N
117
N
C
N
118
N
O
N
119
N
N
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
C
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
H
N
136
N
H
N
137
N
O
N
138
N
P
N
139
N
O
N
140
N
O
N
141
N
O
N
142
N
C
N
143
R
C
N
144
N
O
N
145
S
C
N
146
N
O
N
147
N
C
N
148
R
C
N
149
N
N
N
150
N
C
N
151
N
O
N
152
N
N
N
153
N
C
N
154
N
O
N
155
N
C
N
156
N
C
N
157
N
CL
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
169
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
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
doub
N
28
N
sing
N
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
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
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
Y
67
N
doub
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
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
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
doub
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
doub
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
57
1609
1613
10.1107/S0907444901012318
11679725
Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues
2001
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
91
4160
4164
Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure
1994
10.2210/pdb1idw/pdb
pdb_00001idw
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277
1
mirrors
DIFFRACTOMETER
1997-03-20
ENRAF-NONIUS FAST
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS FR571
2843.149
5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
2
syn
polymer
205.089
RHODIUM HEXAMINE ION
2
syn
non-polymer
35.453
CHLORIDE ION
2
syn
non-polymer
18.015
water
46
nat
water
no
yes
GCUUCGGC(UCL)
GCUUCGGCU
A,B
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
1
2.18
43.66
VAPOR DIFFUSION, SITTING DROP
6.8
cacodylate buffer, MPD, Rhodium-hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
cacodylate buffer
1
MPD
1
rhodium-hexammine
1
MPD
2
0.213
1
19
A
1
B
8
-3.177
A_G1:C8_B
1
-7.216
-0.689
0.220
-0.341
3.982
1
19
A
2
B
7
-1.020
A_C2:G7_B
2
-13.355
0.123
-0.027
-0.139
0.295
28
A
3
B
6
-1.163
A_U3:G6_B
3
-8.164
2.396
0.168
-0.531
2.194
A
4
B
5
-43.178
A_U4:C5_B
4
0.772
-0.552
0.004
0.232
7.951
A
5
B
4
-40.763
A_C5:U4_B
5
-4.351
0.664
-0.444
0.070
-1.934
28
A
6
B
3
-1.535
A_G6:U3_B
6
-11.060
-2.353
-0.282
-0.576
-5.396
1
19
A
7
B
2
-1.176
A_G7:C2_B
7
-11.113
-0.268
-0.043
-0.175
-4.870
1
19
A
8
B
1
-0.551
A_C8:G1_B
8
-5.215
0.307
0.279
-0.147
3.186
35.926
A
A
1
2
1.964
B
B
8
7
3.248
1.211
-0.127
-1.818
AA_G1C2:G7C8_BB
1
0.335
-0.543
35.904
-3.117
0.252
3.221
41.049
A
A
2
3
9.818
B
B
7
6
3.481
6.855
0.071
-1.349
AA_C2U3:G6G7_BB
2
0.271
-0.388
40.496
-2.693
-0.071
3.518
20.414
A
A
3
4
11.728
B
B
6
5
3.289
4.106
-4.109
-1.956
AA_U3U4:C5G6_BB
3
-3.710
10.597
19.658
-7.466
9.833
2.996
38.987
A
A
4
5
12.959
B
B
5
4
3.481
8.582
-0.095
-1.892
AA_U4C5:U4C5_BB
4
1.290
-1.948
38.045
-3.876
0.298
2.516
27.328
A
A
5
6
25.875
B
B
4
3
3.612
11.833
3.175
-1.532
AA_C5G6:U3U4_BB
5
-0.842
1.841
24.663
-6.145
-6.926
3.210
39.743
A
A
6
7
6.803
B
B
3
2
3.444
4.609
0.200
-1.625
AA_G6G7:C2U3_BB
6
-3.719
5.489
39.317
-2.939
-0.737
3.365
34.828
A
A
7
8
0.417
B
B
2
1
3.380
0.250
0.199
-1.910
AA_G7C8:G1C2_BB
7
-0.201
0.336
34.826
-3.230
-0.364
software
diffrn_detector
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Data collection
Database references
Derived calculations
Refinement description
1
0
2001-04-12
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2018-04-18
1
5
2023-08-09
_software.name
_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
A fluoro-Uracil replaces the chloro-uracil at position #9
RCSB
Y
RCSB
2001-04-05
REL
RHD
RHODIUM HEXAMINE ION
CL
CHLORIDE ION
HOH
water
phosphoramidite method
sample
165D
PDB ENTRY 165D
PDB
experimental model
RHD
11
2
RHD
RHD
11
A
RHD
12
2
RHD
RHD
12
A
CL
32
3
CL
CL
32
A
CL
31
3
CL
CL
31
B
HOH
102
4
HOH
HOH
102
A
HOH
103
4
HOH
HOH
103
A
HOH
104
4
HOH
HOH
104
A
HOH
105
4
HOH
HOH
105
A
HOH
106
4
HOH
HOH
106
A
HOH
107
4
HOH
HOH
107
A
HOH
108
4
HOH
HOH
108
A
HOH
110
4
HOH
HOH
110
A
HOH
111
4
HOH
HOH
111
A
HOH
113
4
HOH
HOH
113
A
HOH
114
4
HOH
HOH
114
A
HOH
115
4
HOH
HOH
115
A
HOH
117
4
HOH
HOH
117
A
HOH
118
4
HOH
HOH
118
A
HOH
119
4
HOH
HOH
119
A
HOH
120
4
HOH
HOH
120
A
HOH
121
4
HOH
HOH
121
A
HOH
122
4
HOH
HOH
122
A
HOH
125
4
HOH
HOH
125
A
HOH
131
4
HOH
HOH
131
A
HOH
132
4
HOH
HOH
132
A
HOH
134
4
HOH
HOH
134
A
HOH
137
4
HOH
HOH
137
A
HOH
138
4
HOH
HOH
138
A
HOH
142
4
HOH
HOH
142
A
HOH
143
4
HOH
HOH
143
A
HOH
144
4
HOH
HOH
144
A
HOH
145
4
HOH
HOH
145
A
HOH
101
4
HOH
HOH
101
B
HOH
109
4
HOH
HOH
109
B
HOH
112
4
HOH
HOH
112
B
HOH
116
4
HOH
HOH
116
B
HOH
123
4
HOH
HOH
123
B
HOH
124
4
HOH
HOH
124
B
HOH
126
4
HOH
HOH
126
B
HOH
127
4
HOH
HOH
127
B
HOH
128
4
HOH
HOH
128
B
HOH
129
4
HOH
HOH
129
B
HOH
130
4
HOH
HOH
130
B
HOH
133
4
HOH
HOH
133
B
HOH
135
4
HOH
HOH
135
B
HOH
136
4
HOH
HOH
136
B
HOH
139
4
HOH
HOH
139
B
HOH
140
4
HOH
HOH
140
B
HOH
141
4
HOH
HOH
141
B
HOH
146
4
HOH
HOH
146
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
UCL
9
A
G
1
n
1
G
1
B
C
2
n
2
C
2
B
U
3
n
3
U
3
B
U
4
n
4
U
4
B
C
5
n
5
C
5
B
G
6
n
6
G
6
B
G
7
n
7
G
7
B
C
8
n
8
C
8
B
+U
9
n
9
UCL
9
B
author_defined_assembly
2
dimeric
A
UCL
9
A
UCL
9
DU
B
UCL
9
B
UCL
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
C4'
UCL
9
PLANAR
B
1
-3.64
0.60
125.10
121.46
A
A
A
C6
N1
C2
G
G
G
1
1
1
N
1
4.15
0.60
114.90
119.05
A
A
A
N1
C2
N3
U
U
U
3
3
3
N
1
-4.72
0.60
127.00
122.28
A
A
A
C2
N3
C4
U
U
U
3
3
3
N
1
-3.93
0.60
125.90
121.97
A
A
A
C5
C4
O4
U
U
U
3
3
3
N
1
-4.93
0.60
125.90
120.97
A
A
A
C5
C4
O4
U
U
U
4
4
4
N
1
-2.40
0.40
121.90
119.50
A
A
A
N3
C4
C5
C
C
C
5
5
5
N
1
3.02
0.50
111.50
114.52
A
A
A
C5
C6
N1
G
G
G
6
6
6
N
1
-6.23
0.80
109.40
103.17
A
A
A
O5'
C5'
C4'
G
G
G
7
7
7
N
1
-4.81
0.60
125.10
120.29
B
B
B
C6
N1
C2
G
G
G
1
1
1
N
1
-4.10
0.60
119.90
115.80
B
B
B
N1
C6
O6
G
G
G
1
1
1
N
1
-4.34
0.60
125.90
121.56
B
B
B
C5
C4
O4
U
U
U
3
3
3
N
1
-4.25
0.60
127.00
122.75
B
B
B
C2
N3
C4
U
U
U
4
4
4
N
1
-6.15
0.80
109.40
103.25
B
B
B
O5'
C5'
C4'
G
G
G
6
6
6
N
1
-6.42
0.80
108.20
101.78
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
1
-12.39
1.20
119.70
107.31
B
B
B
C3'
O3'
P
C
C
UCL
8
8
9
A
Y
1
-8.59
1.20
119.70
111.11
B
B
B
C3'
O3'
P
C
C
UCL
8
8
9
B
Y
1
17.68
1.90
104.00
121.68
B
B
B
O3'
P
O5'
C
UCL
UCL
8
9
9
A
A
Y
1
12.75
1.90
104.00
116.75
B
B
B
O3'
P
O5'
C
UCL
UCL
8
9
9
B
B
Y
18.4
Chloro-uracil 9 B disordered at the C2 position.
Refined as two-component 1:1 static orientations
paired to their symmetry-related mates.
The two rhodium atoms are refined anisotropically.
One chlorine atom is disordered.
0.202
0.172
0.176
0.172
1.8
6.0
311
3738
3641
95
RANDOM
1
isotropic
THROUGHOUT
2
4
FOURIER SYNTHESIS
PDB ENTRY 165D
personal dictionary from small molecules
1.8
6.0
46
455
20
389
0
0.011
0.032
0.097
0.071
0.21
0.02
0.169
2.0
40
43.2
0.191
0.02
0.164
2.3
93
98.5
0.211
0.02
0.176
2.7
80
98.7
0.187
0.02
0.168
3.5
69
96.8
0.19
0.02
0.195
6.0
30
76.5
16.4
1.81
6
1IDW
3738
3641
2
4
0.039
0.041
1
18
3.5
97
0.212
1.8
2.
3.0
517
0.206
2.5
43.2
data collection
MADNESS
data reduction
ROTAVATA
phasing
AMoRE
refinement
SHELXL-97
data reduction
MADNESS
data scaling
CCP4
(AGROVATA
data scaling
ROTAVATA
STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF RH(NH3)6+++
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
The second strand of the dimer is not symmetric
covale
1.589
both
A
C
8
A
O3'
C
8
1_555
A
UCL
9
A
P
UCL
9
1_555
covale
1.591
both
A
B
C
8
B
O3'
C
8
1_555
B
UCL
9
B
P
UCL
9
1_555
covale
1.559
both
B
B
C
8
B
O3'
C
8
1_555
B
UCL
9
B
P
UCL
9
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
G
7
B
N1
G
7
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
G
7
B
O6
G
7
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
G
7
B
N2
G
7
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
N3
U
3
1_555
B
G
6
B
O6
G
6
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
O2
U
3
1_555
B
G
6
B
N1
G
6
1_555
hydrog
U-C MISPAIR
A
U
4
A
O4
U
4
1_555
B
C
5
B
N4
C
5
1_555
hydrog
C-U MISPAIR
A
C
5
A
N4
C
5
1_555
B
U
4
B
O4
U
4
1_555
hydrog
TYPE_28_PAIR
A
G
6
A
N1
G
6
1_555
B
U
3
B
O2
U
3
1_555
hydrog
TYPE_28_PAIR
A
G
6
A
O6
G
6
1_555
B
U
3
B
N3
U
3
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
B
C
2
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
C
2
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
C
2
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
1
B
N2
G
1
1_555
DNA/RNA
RNA/DNA HYBRID, RHODIUM HEXAMMINE, C-U MISMATCH, G-U MISMATCH, DNA-RNA COMPLEX
1IDW
PDB
1
1IDW
1
9
1IDW
1
9
1IDW
A
1
1
9
1
9
1IDW
1
9
1IDW
B
1
1
9
BINDING SITE FOR RESIDUE RHD A 11
A
RHD
11
Software
4
BINDING SITE FOR RESIDUE RHD A 12
A
RHD
12
Software
5
A
C
5
A
C
5
4
1_555
A
G
6
A
G
6
4
1_555
A
G
7
A
G
7
4
1_555
A
HOH
106
G
HOH
4
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
5
B
C
5
5
4_546
B
HOH
126
H
HOH
5
4_546
5
C 1 2 1