.033147
.000000
.005108
.000000
.015997
.000000
.000000
.000000
.019865
.00000
.00000
.00000
Szep, S.
Wang, J.
Moore, P.B.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
98.76
90.00
30.169
62.510
50.933
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
Br -1
79.904
BROMIDE ION
non-polymer
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
BR
N
39
N
O
N
40
N
P
N
41
N
O
N
42
N
O
N
43
N
O
N
44
N
C
N
45
R
C
N
46
N
O
N
47
S
C
N
48
N
O
N
49
R
C
N
50
N
O
N
51
R
C
N
52
N
N
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
C
N
57
N
N
N
58
N
C
N
59
N
C
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
H
N
74
N
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
R
C
N
85
N
O
N
86
R
C
Y
87
N
N
Y
88
N
C
Y
89
N
N
Y
90
N
C
N
91
N
C
N
92
N
O
N
93
N
N
N
94
N
C
N
95
N
N
N
96
N
N
Y
97
N
C
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
H
N
112
N
O
N
113
N
H
N
114
N
H
N
115
N
O
N
116
N
P
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
C
N
121
R
C
N
122
N
O
N
123
S
C
N
124
N
O
N
125
R
C
N
126
N
O
N
127
R
C
N
128
N
N
N
129
N
C
N
130
N
O
N
131
N
N
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
C
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
148
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
UK
RNA
RNARFU
2122
1355-8382
9
44
51
10.1261/rna.2107303
12554875
The crystal structure of a 26-nucleotide RNA containing a hook-turn
2003
10.2210/pdb1mhk/pdb
pdb_00001mhk
1.000000
.000000
.000000
.000000
1.000000
.000000
.000000
.000000
1.000000
.00000
.00000
.00000
193
1
193
1
focusing mirrors
IMAGE PLATE
2001-01-31
RIGAKU RAXIS IIC
CCD
2001-04-13
CUSTOM-MADE
focusing mirrors
SINGLE WAVELENGTH
M
x-ray
1
double crystal
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
0.91939
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
X25
NSLS
0.91939
SYNCHROTRON
NSLS BEAMLINE X25
Short strand
3810.352
RNA 12-mer BCh12
fragment of 5S rRNA Loop E
1
syn
polymer
Long strand
4479.691
RNA 14-mer BCh12
fragment of 5S rRNA Loop E
1
syn
polymer
79.904
BROMIDE ION
1
syn
non-polymer
18.015
water
21
nat
water
no
no
CCAUGCGAACCG
CCAUGCGAACCG
S
polyribonucleotide
no
no
CGAUCCUAGUGUGG
CGAUCCUAGUGUGG
L
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.86
57.04
VAPOR DIFFUSION, SITTING DROP
7.5
ammonium sulfate, magnesium chloride, spermidine, tris-hydrogen chloride,
pH 7.5, VAPOR DIFFUSION, SITTING DROP at 292K
292
(NH4)2SO4
1
MgCl2
1
spermidine
1
tris-HCl
1
(NH4)2SO4
2
MgCl2
2
tris-HCl
2
5.486
1
19
S
1
L
14
3.598
S_C1:G14_L
1
-5.863
0.230
0.061
0.037
3.710
1
19
S
2
L
13
1.946
S_C2:G13_L
2
-10.321
0.193
-0.033
0.052
-2.348
1
20
S
3
L
12
4.085
S_A3:U12_L
3
-16.880
0.417
-0.096
0.010
4.210
28
S
4
L
11
-2.437
S_U4:G11_L
4
-12.366
2.236
0.040
-0.603
-4.426
28
S
5
L
10
-0.544
S_G5:U10_L
5
-7.544
-2.519
-0.262
-0.508
3.108
1
19
S
6
L
9
-1.325
S_C6:G9_L
6
-12.388
0.077
-0.013
-0.208
3.994
10
11
S
7
L
8
-4.493
S_G7:A8_L
7
-15.825
6.664
-0.049
-4.470
-1.972
S
8
L
7
-110.074
S_A8:U7_L
8
-6.488
-4.632
0.290
-1.210
-14.178
L
1
L
6
18.219
L_C1:C6_L
9
-15.231
-2.404
0.721
-1.722
-4.003
1
19
L
2
L
5
8.094
L_G2:C5_L
10
-5.311
-1.200
0.042
-0.072
1.334
1
20
L
3
L
4
2.595
L_A3:U4_L
11
-8.800
-0.217
0.364
-0.220
-1.334
1
20
L
4
L
3
2.595
L_U4:A3_L
12
-8.800
0.217
0.364
-0.220
4.003
1
19
L
5
L
2
8.094
L_C5:G2_L
13
-5.311
1.200
0.042
-0.072
14.178
L
6
L
1
18.219
L_C6:C1_L
14
-15.231
2.404
0.721
-1.722
3.038
29.977
S
S
1
2
8.266
L
L
14
13
3.332
4.261
-0.370
-1.958
SS_C1C2:G13G14_LL
1
-0.931
1.807
29.665
-4.646
0.528
2.800
32.907
S
S
2
3
19.182
L
L
13
12
3.433
10.679
-0.331
-1.423
SS_C2A3:U12G13_LL
2
0.631
-1.134
31.165
-4.300
0.691
2.768
37.818
S
S
3
4
12.724
L
L
12
11
3.059
8.186
-0.430
-1.105
SS_A3U4:G11U12_LL
3
-0.777
1.208
36.945
-2.655
0.573
1.125
18.095
S
S
4
5
36.472
L
L
11
10
3.347
10.726
0.439
-2.689
SS_U4G5:U10G11_LL
4
0.316
-1.074
14.590
-13.189
-1.258
3.088
42.240
S
S
5
6
1.538
L
L
10
9
3.124
1.108
-0.069
-1.452
SS_G5C6:G9U10_LL
5
-1.359
1.886
42.206
-2.123
-0.036
3.563
57.005
S
S
6
7
2.453
L
L
9
8
3.594
2.341
-0.830
-0.390
SS_C6G7:A8G9_LL
6
0.964
-1.010
56.954
-0.550
0.927
-0.964
-17.335
S
S
7
8
-14.354
L
L
8
7
3.289
3.968
-5.680
-0.199
SS_G7A8:U7A8_LL
7
-10.705
-38.728
-13.066
-0.342
-21.549
2.766
30.884
L
L
1
2
7.492
L
L
6
5
3.021
3.966
-0.376
-1.189
LL_C1G2:C5C6_LL
8
4.414
-8.337
30.322
-2.920
1.471
2.754
35.391
L
L
2
3
7.877
L
L
5
4
2.985
4.774
0.020
-1.552
LL_G2A3:U4C5_LL
9
-1.179
1.945
35.059
-3.172
-0.185
3.095
36.784
L
L
3
4
4.892
L
L
4
3
3.211
3.084
0.000
-1.305
LL_A3U4:A3U4_LL
10
0.000
0.000
36.659
-2.473
0.000
2.754
35.391
L
L
4
5
7.877
L
L
3
2
2.985
4.774
-0.020
-1.552
LL_U4C5:G2A3_LL
11
1.179
-1.945
35.059
-3.172
0.185
2.766
30.884
L
L
5
6
7.492
L
L
2
1
3.021
3.966
0.376
-1.189
LL_C5C6:C1G2_LL
12
-4.414
8.337
30.322
-2.920
-1.471
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
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-09-06
1
1
2007-10-16
1
2
2011-07-13
1
3
2024-02-14
_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
NDB
Y
RCSB
2002-08-20
REL
BR
BROMIDE ION
HOH
water
5S rRNA Loop E region, sequence from Chromatium minutissimum
sample
5S rRNA Loop E region, sequence from Chromatium minutissimum
sample
6MER
6mer A-form RNA helix
PDB
experimental model
BRO
4
3
BR
BR
13
S
HOH
1
4
HOH
HOH
14
S
HOH
2
4
HOH
HOH
15
S
HOH
3
4
HOH
HOH
16
S
HOH
4
4
HOH
HOH
17
S
HOH
5
4
HOH
HOH
18
S
HOH
9
4
HOH
HOH
19
S
HOH
22
4
HOH
HOH
20
S
HOH
24
4
HOH
HOH
21
S
HOH
28
4
HOH
HOH
22
S
HOH
34
4
HOH
HOH
23
S
HOH
35
4
HOH
HOH
24
S
HOH
6
4
HOH
HOH
15
L
HOH
11
4
HOH
HOH
16
L
HOH
12
4
HOH
HOH
17
L
HOH
14
4
HOH
HOH
18
L
HOH
15
4
HOH
HOH
19
L
HOH
25
4
HOH
HOH
20
L
HOH
27
4
HOH
HOH
21
L
HOH
29
4
HOH
HOH
22
L
HOH
30
4
HOH
HOH
23
L
HOH
32
4
HOH
HOH
24
L
C
1
n
1
C
1
S
C
2
n
2
C
2
S
A
3
n
3
A
3
S
U
4
n
4
U
4
S
G
5
n
5
G
5
S
C
6
n
6
C
6
S
G
7
n
7
G
7
S
A
8
n
8
A
8
S
A
9
n
9
A
9
S
C
10
n
10
C
10
S
C
11
n
11
C
11
S
G
12
n
12
G
12
S
C
1
n
1
C
1
L
G
2
n
2
G
2
L
A
3
n
3
A
3
L
U
4
n
4
U
4
L
C
5
n
5
C
5
L
C
6
n
6
C
6
L
U
7
n
7
U
7
L
A
8
n
8
A
8
L
G
9
n
9
G
9
L
U
10
n
10
U
10
L
G
11
n
11
G
11
L
U
12
n
12
U
12
L
G
13
n
13
G
13
L
G
14
n
14
G
14
L
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
S
HOH
16
D
HOH
1
L
HOH
19
E
HOH
DNA-RNA_REP-BR2.PARAM
DNA-RNA-BR2.TOP
WATER.PARAM
WATER.TOP
ION.PARAM
ION.TOP
55.8
6.17
0.00
20.29
5.29
0.00
-11.46
0.27
0.017
0.2391
0.243
2.50
15.0
252
3217
3011
8.4
93.6
RANDOM
1
RESTRAINED
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
6mer A-form RNA helix
CNS standard parameter files:dna_rnarep.param
FLAT MODEL
54.1757
0.402743
0.49
0.42
5.00
0.57
0.59
2.50
15.0
21
570
1
548
0
0.006
1.08
14.0
1.46
0.335
0.060
0.404
2.66
31
359
6
7.4
78.8
57.5
2.50
15.0
1MHK
3220
1.
0.128
1,2
10.35
17.69
98.6
2.50
2.55
307
0.342
4.59
98.7
data reduction
DENZO
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
Crystal Structure Analysis of a 26mer RNA molecule, representing a new RNA motif, the hook-turn
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
covale
1.875
one
S
U
4
A
C5
U
4
1_555
S
BR
13
C
BR
BR
1_555
hydrog
WATSON-CRICK
S
C
1
A
N3
C
1
1_555
L
G
14
B
N1
G
14
1_555
hydrog
WATSON-CRICK
S
C
1
A
N4
C
1
1_555
L
G
14
B
O6
G
14
1_555
hydrog
WATSON-CRICK
S
C
1
A
O2
C
1
1_555
L
G
14
B
N2
G
14
1_555
hydrog
WATSON-CRICK
S
C
2
A
N3
C
2
1_555
L
G
13
B
N1
G
13
1_555
hydrog
WATSON-CRICK
S
C
2
A
N4
C
2
1_555
L
G
13
B
O6
G
13
1_555
hydrog
WATSON-CRICK
S
C
2
A
O2
C
2
1_555
L
G
13
B
N2
G
13
1_555
hydrog
WATSON-CRICK
S
A
3
A
N1
A
3
1_555
L
U
12
B
N3
U
12
1_555
hydrog
WATSON-CRICK
S
A
3
A
N6
A
3
1_555
L
U
12
B
O4
U
12
1_555
hydrog
TYPE_28_PAIR
S
U
4
A
N3
U
4
1_555
L
G
11
B
O6
G
11
1_555
hydrog
TYPE_28_PAIR
S
U
4
A
O2
U
4
1_555
L
G
11
B
N1
G
11
1_555
hydrog
TYPE_28_PAIR
S
G
5
A
N1
G
5
1_555
L
U
10
B
O2
U
10
1_555
hydrog
TYPE_28_PAIR
S
G
5
A
O6
G
5
1_555
L
U
10
B
N3
U
10
1_555
hydrog
WATSON-CRICK
S
C
6
A
N3
C
6
1_555
L
G
9
B
N1
G
9
1_555
hydrog
WATSON-CRICK
S
C
6
A
N4
C
6
1_555
L
G
9
B
O6
G
9
1_555
hydrog
WATSON-CRICK
S
C
6
A
O2
C
6
1_555
L
G
9
B
N2
G
9
1_555
hydrog
TYPE_11_PAIR
S
G
7
A
N2
G
7
1_555
L
A
8
B
N7
A
8
1_555
hydrog
TYPE_11_PAIR
S
G
7
A
N3
G
7
1_555
L
A
8
B
N6
A
8
1_555
hydrog
A-U PAIR
S
A
8
A
N7
A
8
1_555
L
U
7
B
N3
U
7
1_555
hydrog
A-G MISPAIR
S
A
9
A
N3
A
9
1_555
L
G
9
B
N2
G
9
1_555
hydrog
C-C MISPAIR
L
C
1
B
N4
C
1
1_555
L
C
6
B
N3
C
6
2_556
hydrog
WATSON-CRICK
L
G
2
B
N1
G
2
1_555
L
C
5
B
N3
C
5
2_556
hydrog
WATSON-CRICK
L
G
2
B
N2
G
2
1_555
L
C
5
B
O2
C
5
2_556
hydrog
WATSON-CRICK
L
G
2
B
O6
G
2
1_555
L
C
5
B
N4
C
5
2_556
hydrog
WATSON-CRICK
L
A
3
B
N1
A
3
1_555
L
U
4
B
N3
U
4
2_556
hydrog
WATSON-CRICK
L
A
3
B
N6
A
3
1_555
L
U
4
B
O4
U
4
2_556
hydrog
WATSON-CRICK
L
U
4
B
N3
U
4
1_555
L
A
3
B
N1
A
3
2_556
hydrog
WATSON-CRICK
L
U
4
B
O4
U
4
1_555
L
A
3
B
N6
A
3
2_556
hydrog
WATSON-CRICK
L
C
5
B
N3
C
5
1_555
L
G
2
B
N1
G
2
2_556
hydrog
WATSON-CRICK
L
C
5
B
N4
C
5
1_555
L
G
2
B
O6
G
2
2_556
hydrog
WATSON-CRICK
L
C
5
B
O2
C
5
1_555
L
G
2
B
N2
G
2
2_556
hydrog
C-C MISPAIR
L
C
6
B
N3
C
6
1_555
L
C
1
B
N4
C
1
2_556
RNA
helix, 180 degree turn, RNA
1MHK
PDB
1
1MHK
1MHK
PDB
2
1MHK
1
12
1MHK
1
12
1MHK
S
1
1
12
1
14
1MHK
1
14
1MHK
L
2
1
14
BINDING SITE FOR RESIDUE BR S 13
S
BR
13
Software
2
S
A
3
A
A
3
2
1_555
S
U
4
A
U
4
2
1_555
5
monoclinic
C 1 2 1