0.022032
0.000000
0.000000
0.000000
0.022032
0.000000
0.000000
0.000000
0.019418
0.000000
0.000000
0.000000
Kacer, V.
Scaringe, S.A.
Scarsdale, J.N.
Rife, J.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
45.388
45.388
51.499
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
H2 O
18.015
WATER
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
O
N
112
N
H
N
113
N
H
N
114
N
O
N
115
N
P
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
O
N
122
S
C
N
123
N
O
N
124
R
C
N
125
N
O
N
126
R
C
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
C
N
132
N
O
N
133
N
C
N
134
N
C
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
146
N
H
N
147
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
sing
N
119
N
sing
N
120
N
doub
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
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
59
423
432
10.1107/S0907444902021911
12595698
Crystal structures of r(GGUCACAGCCC)2.
2003
10.2210/pdb1kd5/pdb
pdb_00001kd5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
98
1
CCD
2000-08-20
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
X8C
NSLS
1.000
SYNCHROTRON
NSLS BEAMLINE X8C
3481.146
5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3'
2
syn
polymer
18.015
water
127
nat
water
no
no
GGUCACAGCCC
GGUCACAGCCC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
1
3.23
61.6
VAPOR DIFFUSION, HANGING DROP
6.4
50 mM tris HCl (pH 6.4), 1.4 M (NH4)2SO4, 20 mM MgCl2, 18 mM spermine, neomycin B, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K
293
tris HCl
1
(NH4)2SO4
1
MgCl2
1
spermine
1
neomycin B
1
tris HCl
2
(NH4)2SO4
2
MgCl2
2
spermine
2
-9.606
1
19
A
1
B
10
0.061
A_G1:C10_B
1
-7.684
-0.202
-0.348
0.050
-12.963
1
19
A
2
B
9
-0.210
A_G2:C9_B
2
-11.629
-0.243
-0.259
-0.001
-9.446
28
A
3
B
8
-4.030
A_U3:G8_B
3
-3.829
2.396
0.137
-0.484
-9.748
6
A
4
B
7
-9.293
A_C4:A7_B
4
7.287
7.095
0.444
-4.159
-2.824
4
25
A
5
B
6
-97.780
A_A5:C6_B
5
-11.622
-3.187
-0.185
0.056
3.771
4
25
A
6
B
5
-96.196
A_C6:A5_B
6
-9.922
3.103
-0.089
0.024
10.141
6
A
7
B
4
-9.472
A_A7:C4_B
7
8.747
-7.126
0.455
-4.218
8.327
28
A
8
B
3
-3.801
A_G8:U3_B
8
-2.648
-2.377
0.081
-0.485
13.895
1
19
A
9
B
2
-0.129
A_C9:G2_B
9
-12.247
0.239
-0.248
0.052
8.637
1
19
A
10
B
1
-0.064
A_C10:G1_B
10
-5.644
0.197
-0.280
0.025
3.122
31.436
A
A
1
2
9.585
B
B
10
9
3.495
5.169
0.040
-2.034
AA_G1G2:C9C10_BB
1
1.262
-2.340
30.994
-4.740
0.167
3.107
42.097
A
A
2
3
5.780
B
B
9
8
3.246
4.146
0.087
-1.313
AA_G2U3:G8C9_BB
2
-0.248
0.346
41.901
-2.245
-0.146
3.327
58.380
A
A
3
4
6.785
B
B
8
7
3.456
6.592
0.345
-1.227
AA_U3C4:A7G8_BB
3
7.304
-7.518
57.617
-1.618
0.047
4.161
-12.152
A
A
4
5
7.873
B
B
7
6
2.983
-1.642
-5.470
-1.011
AA_C4A5:C6A7_BB
4
3.231
15.498
-11.601
7.100
-21.266
3.436
66.250
A
A
5
6
-3.890
B
B
6
5
3.228
-4.249
0.001
-3.751
AA_A5C6:A5C6_BB
5
-0.297
0.272
66.128
-3.258
-0.013
4.021
-12.121
A
A
6
7
12.067
B
B
5
4
2.978
-2.500
5.442
-1.008
AA_C6A7:C4A5_BB
6
-3.171
-15.305
-11.432
8.279
21.325
3.344
59.252
A
A
7
8
7.010
B
B
4
3
3.474
6.903
-0.354
-1.208
AA_A7G8:U3C4_BB
7
-7.299
7.412
58.470
-1.590
-0.031
3.076
41.359
A
A
8
9
5.495
B
B
3
2
3.207
3.876
-0.086
-1.322
AA_G8C9:G2U3_BB
8
-0.048
0.068
41.185
-2.271
0.117
3.148
31.753
A
A
9
10
9.829
B
B
2
1
3.539
5.351
-0.053
-2.070
AA_C9C10:G1G2_BB
9
-1.719
3.157
31.265
-4.794
-0.228
chem_comp_atom
chem_comp_bond
database_2
software
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Refinement description
1
0
2003-03-04
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_software.name
NDB
Y
RCSB
2001-11-12
REL
REL
HOH
water
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
31
2
HOH
HOH
31
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
37
2
HOH
HOH
37
A
HOH
38
2
HOH
HOH
38
A
HOH
41
2
HOH
HOH
41
A
HOH
42
2
HOH
HOH
42
A
HOH
46
2
HOH
HOH
46
A
HOH
47
2
HOH
HOH
47
A
HOH
51
2
HOH
HOH
51
A
HOH
53
2
HOH
HOH
53
A
HOH
54
2
HOH
HOH
54
A
HOH
56
2
HOH
HOH
56
A
HOH
59
2
HOH
HOH
59
A
HOH
60
2
HOH
HOH
60
A
HOH
63
2
HOH
HOH
63
A
HOH
64
2
HOH
HOH
64
A
HOH
65
2
HOH
HOH
65
A
HOH
67
2
HOH
HOH
67
A
HOH
71
2
HOH
HOH
71
A
HOH
73
2
HOH
HOH
73
A
HOH
75
2
HOH
HOH
75
A
HOH
78
2
HOH
HOH
78
A
HOH
79
2
HOH
HOH
79
A
HOH
82
2
HOH
HOH
82
A
HOH
87
2
HOH
HOH
87
A
HOH
88
2
HOH
HOH
88
A
HOH
92
2
HOH
HOH
92
A
HOH
94
2
HOH
HOH
94
A
HOH
95
2
HOH
HOH
95
A
HOH
96
2
HOH
HOH
96
A
HOH
97
2
HOH
HOH
97
A
HOH
98
2
HOH
HOH
98
A
HOH
102
2
HOH
HOH
102
A
HOH
104
2
HOH
HOH
104
A
HOH
105
2
HOH
HOH
105
A
HOH
107
2
HOH
HOH
107
A
HOH
108
2
HOH
HOH
108
A
HOH
110
2
HOH
HOH
110
A
HOH
112
2
HOH
HOH
112
A
HOH
118
2
HOH
HOH
118
A
HOH
120
2
HOH
HOH
120
A
HOH
121
2
HOH
HOH
121
A
HOH
122
2
HOH
HOH
122
A
HOH
124
2
HOH
HOH
124
A
HOH
126
2
HOH
HOH
126
A
HOH
131
2
HOH
HOH
131
A
HOH
132
2
HOH
HOH
132
A
HOH
133
2
HOH
HOH
133
A
HOH
136
2
HOH
HOH
136
A
HOH
137
2
HOH
HOH
137
A
HOH
138
2
HOH
HOH
138
A
HOH
139
2
HOH
HOH
139
A
HOH
141
2
HOH
HOH
141
A
HOH
144
2
HOH
HOH
144
A
HOH
145
2
HOH
HOH
145
A
HOH
146
2
HOH
HOH
146
A
HOH
150
2
HOH
HOH
150
A
HOH
152
2
HOH
HOH
152
A
HOH
155
2
HOH
HOH
155
A
HOH
156
2
HOH
HOH
156
A
HOH
26
2
HOH
HOH
26
B
HOH
29
2
HOH
HOH
29
B
HOH
30
2
HOH
HOH
30
B
HOH
32
2
HOH
HOH
32
B
HOH
33
2
HOH
HOH
33
B
HOH
39
2
HOH
HOH
39
B
HOH
40
2
HOH
HOH
40
B
HOH
43
2
HOH
HOH
43
B
HOH
44
2
HOH
HOH
44
B
HOH
45
2
HOH
HOH
45
B
HOH
48
2
HOH
HOH
48
B
HOH
49
2
HOH
HOH
49
B
HOH
50
2
HOH
HOH
50
B
HOH
52
2
HOH
HOH
52
B
HOH
55
2
HOH
HOH
55
B
HOH
57
2
HOH
HOH
57
B
HOH
58
2
HOH
HOH
58
B
HOH
61
2
HOH
HOH
61
B
HOH
62
2
HOH
HOH
62
B
HOH
66
2
HOH
HOH
66
B
HOH
68
2
HOH
HOH
68
B
HOH
69
2
HOH
HOH
69
B
HOH
70
2
HOH
HOH
70
B
HOH
72
2
HOH
HOH
72
B
HOH
74
2
HOH
HOH
74
B
HOH
76
2
HOH
HOH
76
B
HOH
77
2
HOH
HOH
77
B
HOH
80
2
HOH
HOH
80
B
HOH
81
2
HOH
HOH
81
B
HOH
83
2
HOH
HOH
83
B
HOH
84
2
HOH
HOH
84
B
HOH
85
2
HOH
HOH
85
B
HOH
86
2
HOH
HOH
86
B
HOH
89
2
HOH
HOH
89
B
HOH
90
2
HOH
HOH
90
B
HOH
91
2
HOH
HOH
91
B
HOH
93
2
HOH
HOH
93
B
HOH
99
2
HOH
HOH
99
B
HOH
100
2
HOH
HOH
100
B
HOH
101
2
HOH
HOH
101
B
HOH
103
2
HOH
HOH
103
B
HOH
106
2
HOH
HOH
106
B
HOH
109
2
HOH
HOH
109
B
HOH
111
2
HOH
HOH
111
B
HOH
113
2
HOH
HOH
113
B
HOH
114
2
HOH
HOH
114
B
HOH
116
2
HOH
HOH
116
B
HOH
117
2
HOH
HOH
117
B
HOH
119
2
HOH
HOH
119
B
HOH
123
2
HOH
HOH
123
B
HOH
125
2
HOH
HOH
125
B
HOH
127
2
HOH
HOH
127
B
HOH
128
2
HOH
HOH
128
B
HOH
129
2
HOH
HOH
129
B
HOH
130
2
HOH
HOH
130
B
HOH
134
2
HOH
HOH
134
B
HOH
135
2
HOH
HOH
135
B
HOH
140
2
HOH
HOH
140
B
HOH
142
2
HOH
HOH
142
B
HOH
143
2
HOH
HOH
143
B
HOH
147
2
HOH
HOH
147
B
HOH
148
2
HOH
HOH
148
B
HOH
149
2
HOH
HOH
149
B
G
1
n
1
G
1
A
G
2
n
2
G
2
A
U
3
n
3
U
3
A
C
4
n
4
C
4
A
A
5
n
5
A
5
A
C
6
n
6
C
6
A
A
7
n
7
A
7
A
G
8
n
8
G
8
A
C
9
n
9
C
9
A
C
10
n
10
C
10
A
C
11
n
11
C
11
A
G
1
n
1
G
1
B
G
2
n
2
G
2
B
U
3
n
3
U
3
B
C
4
n
4
C
4
B
A
5
n
5
A
5
B
C
6
n
6
C
6
B
A
7
n
7
A
7
B
G
8
n
8
G
8
B
C
9
n
9
C
9
B
C
10
n
10
C
10
B
C
11
n
11
C
11
B
0.1569
0.1714
0.1569
0.1714
0.226
0.226
1324
13.9
9475
12429
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
-2.46
0.40
120.30
117.84
A
A
A
C6
N1
C2
C
C
C
4
4
4
N
1
5.33
0.70
108.50
113.83
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
1
3.81
0.50
111.90
115.71
A
A
A
C2
N3
C4
G
G
G
8
8
8
N
1
-3.89
0.50
128.60
124.71
A
A
A
N3
C4
C5
G
G
G
8
8
8
N
1
-3.15
0.40
120.30
117.15
A
A
A
C6
N1
C2
C
C
C
10
10
10
N
1
3.66
0.50
111.90
115.56
B
B
B
C2
N3
C4
G
G
G
8
8
8
N
1
-3.52
0.50
128.60
125.08
B
B
B
N3
C4
C5
G
G
G
8
8
8
N
1
B
B
N7
C8
G
G
2
2
0.037
0.006
1.305
1.342
N
Preliminary refinement in CNS.
Restrained Anisotropic B factors as implemented in SHELXL-96
0.226
0.1714
0.174
0.1714
1.58
5.00
5286
1324
13324
6608
9.93
96.4
random
1
Restrained Anisotropic B factors as implemented in SHELXL-96
THROUGHOUT
2.0
SIRAS
MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-227
0.164
5.00
0
0.00
587.00
1.58
5.00
127
587
0
460
0
0.013
0.028
0.037
0.016
1.58
25
1KD5
14792
14143
-3
0.058
1
17.7
5.4
95.6
0.558
1.58
1.67
1.7
721
2.2
91.7
data reduction
DENZO
data scaling
SCALEPACK
phasing
SHARP
refinement
SHELXL
The Crystal Structure of r(GGUCACAGCCC)2 metal free form
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
10
B
N3
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
10
B
O2
C
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
10
B
N4
C
10
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
9
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
9
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
9
B
N4
C
9
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
N3
U
3
1_555
B
G
8
B
O6
G
8
1_555
hydrog
TYPE_28_PAIR
A
U
3
A
O2
U
3
1_555
B
G
8
B
N1
G
8
1_555
hydrog
C-A MISPAIR
A
C
4
A
O2
C
4
1_555
B
A
7
B
N6
A
7
1_555
hydrog
TYPE_25_PAIR
A
A
5
A
N6
A
5
1_555
B
C
6
B
N3
C
6
1_555
hydrog
TYPE_25_PAIR
A
A
5
A
N7
A
5
1_555
B
C
6
B
N4
C
6
1_555
hydrog
TYPE_25_PAIR
A
C
6
A
N3
C
6
1_555
B
A
5
B
N6
A
5
1_555
hydrog
TYPE_25_PAIR
A
C
6
A
N4
C
6
1_555
B
A
5
B
N7
A
5
1_555
hydrog
A-C MISPAIR
A
A
7
A
N6
A
7
1_555
B
C
4
B
O2
C
4
1_555
hydrog
TYPE_28_PAIR
A
G
8
A
N1
G
8
1_555
B
U
3
B
O2
U
3
1_555
hydrog
TYPE_28_PAIR
A
G
8
A
O6
G
8
1_555
B
U
3
B
N3
U
3
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
G
2
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
G
2
B
O6
G
2
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
G
2
B
N2
G
2
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
10
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
10
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
10
1_555
B
G
1
B
N2
G
1
1_555
RNA
RNA duplex, RNA
1KD5
PDB
1
1KD5
1
11
1KD5
1
11
1KD5
A
1
1
11
1
11
1KD5
1
11
1KD5
B
1
1
11
78
tetragonal
P 43