0.023992
0.013852
0.000000
0.000000
0.027703
0.000000
0.000000
0.000000
0.016663
0.00000
0.00000
0.00000
Jiang, S.
Sun, H.
Gan, J.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
41.681
41.681
60.014
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 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
Sr 2
87.620
STRONTIUM ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA 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
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
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
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
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
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
SR
N
112
N
O
N
113
N
P
N
114
N
O
N
115
N
O
N
116
N
O
N
117
N
C
N
118
R
C
N
119
N
O
N
120
S
C
N
121
N
O
N
122
R
C
N
123
N
O
N
124
R
C
N
125
N
N
N
126
N
C
N
127
N
O
N
128
N
N
N
129
N
C
N
130
N
O
N
131
N
C
N
132
N
C
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
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
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
doub
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
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
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
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
To be Published
0353
2-Se Uridine enhanced U/G Wobble Base Pair Discrimination
10.2210/pdb4jab/pdb
pdb_00004jab
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2012-12-14
ADSC QUANTUM 315
Double crystal, Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.97895
1.0
8.2.2
ALS
0.97895
SYNCHROTRON
ALS BEAMLINE 8.2.2
2527.545
RNA (5'-R(*GP*UP*GP*UP*AP*UP*AP*C)-3')
2
syn
polymer
87.620
STRONTIUM ION
5
syn
non-polymer
no
no
GUGUAUAC
GUGUAUAC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
1
1.98
38.02
VAPOR DIFFUSION, HANGING DROP
VAPOR DIFFUSION, HANGING DROP
4.107
1
A
1
B
16
-0.463
A_G1:C16_B
1
-13.157
0.133
0.944
0.373
5.236
1
20
A
2
B
15
-3.132
A_U2:A15_B
2
-22.484
0.356
0.361
-0.123
0.122
1
28
A
3
B
14
11.040
A_G3:U14_B
3
-16.955
-1.677
0.507
-0.112
-0.406
1
20
A
4
B
13
6.075
A_U4:A13_B
4
-15.915
-0.179
0.373
0.168
0.737
1
20
A
5
B
12
2.344
A_A5:U12_B
5
-19.878
0.133
0.440
-0.186
-1.655
1
28
A
6
B
11
2.342
A_U6:G11_B
6
-22.553
2.554
0.863
-0.504
4.436
1
20
A
7
B
10
2.080
A_A7:U10_B
7
-14.834
0.020
0.355
0.001
5.728
1
19
A
8
B
9
-4.456
A_C8:G9_B
8
-18.153
0.651
0.155
-0.093
2.638
35.901
A
A
1
2
16.849
B
B
16
15
3.174
10.235
-0.306
-1.335
AA_G1U2:A15C16_BB
1
3.424
-5.637
34.291
-3.499
0.943
2.398
29.901
A
A
2
3
18.968
B
B
15
14
2.962
9.618
1.268
-1.174
AA_U2G3:U14A15_BB
2
-0.998
1.968
28.328
-3.954
-2.633
2.993
35.281
A
A
3
4
9.603
B
B
14
13
3.213
5.794
-0.475
-1.220
AA_G3U4:A13U14_BB
3
-1.251
2.073
34.795
-2.833
0.606
2.847
36.775
A
A
4
5
8.081
B
B
13
12
3.050
5.083
-0.086
-1.326
AA_U4A5:U12A13_BB
4
-0.745
1.184
36.427
-2.729
0.045
2.817
43.802
A
A
5
6
12.713
B
B
12
11
3.133
9.417
-0.176
-1.213
AA_A5U6:G11U12_BB
5
0.202
-0.272
42.826
-2.451
0.253
1.667
30.825
A
A
6
7
25.107
B
B
11
10
2.610
12.885
-0.814
-1.313
AA_U6A7:U10G11_BB
6
5.226
-10.183
27.579
-4.210
2.237
2.892
35.984
A
A
7
8
17.603
B
B
10
9
3.267
10.703
0.474
-0.921
AA_A7C8:G9U10_BB
7
3.604
-5.928
34.222
-2.965
-0.271
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
Refinement description
1
0
2014-01-29
1
1
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-02-18
REL
REL
SR
STRONTIUM ION
32630
synthetic construct
sample
246D
PDB ENTRY 246D
PDB
experimental model
SR
1
2
SR
SR
101
A
SR
1
2
SR
SR
102
A
SR
1
2
SR
SR
103
A
SR
1
2
SR
SR
104
A
SR
1
2
SR
SR
101
B
G
1
n
1
G
1
A
U
2
n
2
U
2
A
G
3
n
3
G
3
A
U
4
n
4
U
4
A
A
5
n
5
A
5
A
U
6
n
6
U
6
A
A
7
n
7
A
7
A
C
8
n
8
C
8
A
G
9
n
1
G
9
B
U
10
n
2
U
10
B
G
11
n
3
G
11
B
U
12
n
4
U
12
B
A
13
n
5
A
13
B
U
14
n
6
U
14
B
A
15
n
7
A
15
B
C
16
n
8
C
16
B
author_and_software_defined_assembly
PISA
2
dimeric
1630
-118
2830
A
C
8
A
O2'
C
8
1_555
A
SR
103
E
SR
SR
1_555
A
C
8
A
O3'
C
8
1_555
64.8
A
C
8
A
O2'
C
8
1_555
A
SR
103
E
SR
SR
1_555
A
C
8
A
O3'
C
8
1_555
64.8
A
C
8
A
O3'
C
8
1_555
A
SR
103
E
SR
SR
1_555
A
C
8
A
O3'
C
8
1_555
0.0
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
-7.81
1.20
119.70
111.89
A
A
A
C3'
O3'
P
G
G
U
3
3
4
Y
1
-11.03
1.20
119.70
108.67
B
B
B
C3'
O3'
P
G
G
U
11
11
12
Y
32.957
-7.33
-0.00
-0.00
-7.33
-0.00
14.67
0.981
0.958
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.22898
0.15250
0.15648
2.23
30.93
73
1893
1650
4.2
91.02
22.870
0.222
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.051
0.80
0.80
1.20
PDB ENTRY 246D
MAXIMUM LIKELIHOOD
MASK
2.23
30.93
0
339
5
334
0
0.009
0.011
372
2.093
1.452
576
0.111
0.200
64
0.012
0.020
164
6.192
3.000
372
68.134
5.000
3
41.320
5.000
336
0.561
0.340
2.288
5
112
20
90.70
2.23
30.93
4JAB
1893
1723
2
-3
0.066
1
2.2
91.02
0.33
2.23
2.31
1
2
90.1
data collection
HKL-2000
phasing
PHASER
refinement
REFMAC
5.6.0117
data reduction
HKL-2000
data scaling
HKL-2000
U/G Wobble Base Pair in a RNA Duplex
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
metalc
2.741
A
U
6
A
O4
U
6
1_555
A
SR
102
D
SR
SR
1_555
metalc
2.330
A
C
8
A
O2'
C
8
1_555
A
SR
103
E
SR
SR
1_555
metalc
2.609
A
C
8
A
O3'
C
8
1_555
A
SR
103
E
SR
SR
1_555
metalc
1.992
A
C
8
A
O3'
C
8
1_555
A
SR
103
E
SR
SR
2_545
metalc
2.467
B
U
14
B
O4
U
6
1_555
B
SR
101
G
SR
SR
1_555
hydrog
G-A MISPAIR
A
G
1
A
O6
G
1
1_555
B
A
15
B
N6
A
7
1_555
hydrog
G-C PAIR
A
G
1
A
N1
G
1
1_555
B
C
16
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
U
2
A
N3
U
2
1_555
B
A
15
B
N1
A
7
1_555
hydrog
WATSON-CRICK
A
U
2
A
O4
U
2
1_555
B
A
15
B
N6
A
7
1_555
hydrog
TYPE_28_PAIR
A
G
3
A
N1
G
3
1_555
B
U
14
B
O2
U
6
1_555
hydrog
TYPE_28_PAIR
A
G
3
A
O6
G
3
1_555
B
U
14
B
N3
U
6
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
4
1_555
B
A
13
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
4
1_555
B
A
13
B
N6
A
5
1_555
hydrog
A-G MISPAIR
A
A
5
A
N6
A
5
1_555
B
G
11
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
A
5
A
N1
A
5
1_555
B
U
12
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
A
5
A
N6
A
5
1_555
B
U
12
B
O4
U
4
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
N3
U
6
1_555
B
G
11
B
O6
G
3
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
O2
U
6
1_555
B
G
11
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
A
7
A
N1
A
7
1_555
B
U
10
B
N3
U
2
1_555
hydrog
WATSON-CRICK
A
A
7
A
N6
A
7
1_555
B
U
10
B
O4
U
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
9
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
9
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
9
B
N2
G
1
1_555
RNA
U/G wobble pair, RNA
4JAB
PDB
1
4JAB
1
8
4JAB
1
8
4JAB
A
1
1
8
9
16
4JAB
9
16
4JAB
B
1
1
8
BINDING SITE FOR RESIDUE SR A 101
A
SR
101
Software
1
BINDING SITE FOR RESIDUE SR A 102
A
SR
102
Software
1
BINDING SITE FOR RESIDUE SR A 103
A
SR
103
Software
3
BINDING SITE FOR RESIDUE SR B 101
B
SR
101
Software
1
A
U
4
A
U
4
1
1_555
A
U
6
A
U
6
1
1_555
A
C
8
A
C
8
3
1_555
A
C
8
A
C
8
3
2_545
A
C
8
A
C
8
3
3_655
B
U
14
B
U
6
1
1_555
146
H 3