0.027812
0.000000
0.000000
0.000000
0.027812
0.000000
0.000000
0.000000
0.026285
0.00000
0.00000
0.00000
Pan, B.C.
Xiong, Y.
Shi, K.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
35.956
35.956
38.045
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H13 Br N5 O7 P
426.117
n
8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
Na 1
22.990
SODIUM ION
non-polymer
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
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
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
R
C
Y
46
N
N
Y
47
N
C
Y
48
N
N
Y
49
N
C
Y
50
N
C
N
51
N
N
N
52
N
C
N
53
N
N
N
54
N
N
N
55
N
C
N
56
N
O
N
57
N
C
N
58
S
C
N
59
N
O
N
60
N
O
N
61
N
BR
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
P
N
77
N
O
N
78
N
O
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
O
N
83
S
C
N
84
N
O
N
85
R
C
N
86
N
O
N
87
R
C
Y
88
N
N
Y
89
N
C
Y
90
N
N
Y
91
N
C
N
92
N
C
N
93
N
O
N
94
N
N
N
95
N
C
N
96
N
N
N
97
N
N
Y
98
N
C
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
H
N
113
N
O
N
114
N
H
N
115
N
H
N
116
N
NA
N
117
N
CO
N
118
N
N
N
119
N
N
N
120
N
N
N
121
N
N
N
122
N
N
N
123
N
N
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
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
O
N
143
N
P
N
144
N
O
N
145
N
O
N
146
N
O
N
147
N
C
N
148
R
C
N
149
N
O
N
150
S
C
N
151
N
O
N
152
R
C
N
153
N
O
N
154
R
C
N
155
N
N
N
156
N
C
N
157
N
O
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
C
N
162
N
C
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
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
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
doub
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
Y
56
N
sing
Y
57
N
sing
Y
58
N
doub
N
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
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
doub
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
Y
103
N
sing
Y
104
N
sing
Y
105
N
doub
N
106
N
sing
Y
107
N
sing
N
108
N
sing
Y
109
N
doub
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
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
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
doub
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
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
doub
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
doub
N
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
UK
Structure
STRUE6
2005
0969-2126
11
825
831
10.1016/S0969-2126(03)00108-4
12842045
An Eight-Stranded Helical Fragment in RNA Crystal Structure: Implications for Tetraplex Interaction
2003
10.2210/pdb1mdg/pdb
pdb_00001mdg
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
105
1
mirrors
CCD
2001-05-31
ENRAF-NONIUS
graphite
MAD
M
x-ray
1
0.9195
1.0
0.9192
1.0
0.800
1.0
14-BM-D
APS
0.9195, 0.9192, 0.800
SYNCHROTRON
APS BEAMLINE 14-BM-D
1995.093
5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'
1
syn
polymer
22.990
SODIUM ION
5
syn
non-polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
18.015
water
16
nat
water
no
yes
U(BGM)AGGU
UGAGGU
A
polyribonucleotide
n
n
n
n
n
n
1
1.54
20.17
VAPOR DIFFUSION, HANGING DROP
6.6
MPD, MgCl2, Cobalt(III)hexammine, ethidine bromide, sodium cacodylate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
MPD
1
MgCl2
1
Cobalt(III)hexammine
1
ethidine bromide
1
sodium cacodylate
1
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
1
0
2003-08-12
1
1
2008-04-28
1
2
2011-07-13
1
3
2011-09-28
1
4
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-08-07
REL
REL
NA
SODIUM ION
NCO
COBALT HEXAMMINE(III)
HOH
water
NA1
101
2
NA
NA
101
A
NA1
102
2
NA
NA
102
A
NA1
103
2
NA
NA
103
A
NA1
104
2
NA
NA
104
A
NA1
105
2
NA
NA
105
A
COB
201
3
NCO
NCO
201
A
WAT
301
4
HOH
HOH
301
A
WAT
302
4
HOH
HOH
302
A
WAT
303
4
HOH
HOH
303
A
WAT
304
4
HOH
HOH
304
A
WAT
305
4
HOH
HOH
305
A
WAT
316
4
HOH
HOH
306
A
WAT
307
4
HOH
HOH
307
A
WAT
308
4
HOH
HOH
308
A
WAT
309
4
HOH
HOH
309
A
WAT
310
4
HOH
HOH
310
A
WAT
312
4
HOH
HOH
312
A
WAT
313
4
HOH
HOH
313
A
WAT
314
4
HOH
HOH
314
A
WAT
315
4
HOH
HOH
315
A
WAT
317
4
HOH
HOH
316
A
WAT
411
4
HOH
HOH
411
A
URI
1
n
1
U
1
A
GUA
2
n
2
BGM
2
A
ADE
3
n
3
A
3
A
GUA
4
n
4
G
4
A
GUA
5
n
5
G
5
A
URI
6
n
6
U
6
A
author_defined_assembly
4
tetrameric
A
G
4
A
O6
G
4
1_555
A
NA
104
E
NA
NA
1_555
A
G
5
A
O6
G
5
1_555
71.8
A
G
5
A
O6
G
5
1_555
A
NA
105
F
NA
NA
1_555
A
U
6
A
O4
U
6
1_555
69.7
A
BGM
2
A
BGM
2
DG
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_555
-y,x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_555
y,-x,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
NA
101
B
NA
1
A
NA
102
C
NA
1
A
NA
103
D
NA
1
A
NA
104
E
NA
1
A
NA
105
F
NA
1
A
NCO
201
G
NCO
1
A
HOH
305
H
HOH
1
A
HOH
315
H
HOH
1
A
G
4
0.064
SIDE CHAIN
1
29.06
1.60
113.70
142.76
A
A
A
C2'
C3'
O3'
U
U
U
6
6
6
N
1
-10.37
1.00
105.80
95.43
A
A
A
O4'
C1'
C2'
U
U
U
6
6
6
N
1
-31.93
1.10
112.00
80.07
A
A
A
N1
C1'
C2'
U
U
U
6
6
6
N
1
22.72
3.00
110.60
133.32
A
A
A
C1'
C2'
O2'
U
U
U
6
6
6
N
1
-30.86
2.90
113.30
82.44
A
A
A
C3'
C2'
O2'
U
U
U
6
6
6
N
0.194
0.172
1.50
30.0
381
3821
3763
98.5
random
1
isotropic
2.0
MAD
Engh & Huber
1.50
30.0
16
156
12
128
0
1.5
30.0
1MDG
3807
3800
2.0
2.0
0.056
1
41.7
99.8
1.50
1.55
364
0.309
1
98.6
data reduction
DENZO
data scaling
SCALEPACK
refinement
CNS
phasing
CNS
An Alternating Antiparallel Octaplex in an RNA Crystal Structure
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
The three strands of the tetraplex is generated by the four fold axis
covale
1.592
both
A
U
1
A
O3'
U
1
1_555
A
BGM
2
A
P
BGM
2
1_555
covale
1.633
both
A
BGM
2
A
O3'
BGM
2
1_555
A
A
3
A
P
A
3
1_555
metalc
2.865
A
BGM
2
A
O6
BGM
2
1_555
A
NA
101
B
NA
NA
1_555
metalc
2.823
A
BGM
2
A
O6
BGM
2
1_555
A
NA
102
C
NA
NA
1_555
metalc
2.995
A
G
4
A
O6
G
4
1_555
A
NA
103
D
NA
NA
1_555
metalc
2.752
A
G
4
A
O6
G
4
1_555
A
NA
104
E
NA
NA
1_555
metalc
2.749
A
G
5
A
O6
G
5
1_555
A
NA
104
E
NA
NA
1_555
metalc
2.830
A
G
5
A
O6
G
5
1_555
A
NA
105
F
NA
NA
1_555
metalc
2.703
A
U
6
A
O4
U
6
1_555
A
NA
105
F
NA
NA
1_555
RNA
tetraplex, base tetrads, base octads, RNA
1MDG
PDB
1
1MDG
1
6
1MDG
1
6
1MDG
A
1
1
6
BINDING SITE FOR RESIDUE NA A 101
A
NA
101
Software
16
BINDING SITE FOR RESIDUE NA A 102
A
NA
102
Software
20
BINDING SITE FOR RESIDUE NA A 103
A
NA
103
Software
16
BINDING SITE FOR RESIDUE NA A 104
A
NA
104
Software
16
BINDING SITE FOR RESIDUE NA A 105
A
NA
105
Software
12
BINDING SITE FOR RESIDUE NCO A 201
A
NCO
201
Software
12
A
BGM
2
A
BGM
2
16
3_555
A
BGM
2
A
BGM
2
16
6_556
A
BGM
2
A
BGM
2
16
7_556
A
BGM
2
A
BGM
2
16
1_555
A
BGM
2
A
BGM
2
16
4_555
A
BGM
2
A
BGM
2
16
5_556
A
BGM
2
A
BGM
2
16
2_555
A
BGM
2
A
BGM
2
16
8_556
A
NA
102
C
NA
16
4_555
A
NA
102
C
NA
16
5_556
A
NA
102
C
NA
16
6_556
A
NA
102
C
NA
16
7_556
A
NA
102
C
NA
16
8_556
A
NA
102
C
NA
16
3_555
A
NA
102
C
NA
16
2_555
A
NA
102
C
NA
16
1_555
A
BGM
2
A
BGM
2
20
3_555
A
BGM
2
A
BGM
2
20
1_555
A
BGM
2
A
BGM
2
20
2_555
A
BGM
2
A
BGM
2
20
4_555
A
A
3
A
A
3
20
3_555
A
A
3
A
A
3
20
2_555
A
A
3
A
A
3
20
1_555
A
A
3
A
A
3
20
4_555
A
NA
101
B
NA
20
4_555
A
NA
101
B
NA
20
3_555
A
NA
101
B
NA
20
1_555
A
NA
101
B
NA
20
2_555
A
NA
101
B
NA
20
5_556
A
NA
101
B
NA
20
6_556
A
NA
101
B
NA
20
7_556
A
NA
101
B
NA
20
8_556
A
NA
103
D
NA
20
4_555
A
NA
103
D
NA
20
3_555
A
NA
103
D
NA
20
2_555
A
NA
103
D
NA
20
1_555
A
A
3
A
A
3
16
3_555
A
A
3
A
A
3
16
1_555
A
A
3
A
A
3
16
2_555
A
A
3
A
A
3
16
4_555
A
G
4
A
G
4
16
4_555
A
G
4
A
G
4
16
1_555
A
G
4
A
G
4
16
2_555
A
G
4
A
G
4
16
3_555
A
NA
102
C
NA
16
3_555
A
NA
102
C
NA
16
1_555
A
NA
102
C
NA
16
2_555
A
NA
102
C
NA
16
4_555
A
NA
104
E
NA
16
4_555
A
NA
104
E
NA
16
3_555
A
NA
104
E
NA
16
2_555
A
NA
104
E
NA
16
1_555
A
G
4
A
G
4
16
2_555
A
G
4
A
G
4
16
4_555
A
G
4
A
G
4
16
1_555
A
G
4
A
G
4
16
3_555
A
G
5
A
G
5
16
2_555
A
G
5
A
G
5
16
4_555
A
G
5
A
G
5
16
1_555
A
G
5
A
G
5
16
3_555
A
NA
103
D
NA
16
1_555
A
NA
103
D
NA
16
2_555
A
NA
103
D
NA
16
3_555
A
NA
103
D
NA
16
4_555
A
NA
105
F
NA
16
4_555
A
NA
105
F
NA
16
3_555
A
NA
105
F
NA
16
2_555
A
NA
105
F
NA
16
1_555
A
G
5
A
G
5
12
2_555
A
G
5
A
G
5
12
3_555
A
G
5
A
G
5
12
1_555
A
G
5
A
G
5
12
4_555
A
U
6
A
U
6
12
2_555
A
U
6
A
U
6
12
1_555
A
U
6
A
U
6
12
3_555
A
U
6
A
U
6
12
4_555
A
NA
104
E
NA
12
4_555
A
NA
104
E
NA
12
3_555
A
NA
104
E
NA
12
2_555
A
NA
104
E
NA
12
1_555
A
BGM
2
A
BGM
2
12
1_555
A
BGM
2
A
BGM
2
12
8_556
A
A
3
A
A
3
12
8_556
A
A
3
A
A
3
12
1_555
A
G
5
A
G
5
12
14_455
A
G
5
A
G
5
12
12_455
A
U
6
A
U
6
12
12_455
A
U
6
A
U
6
12
14_455
A
HOH
308
H
HOH
12
8_556
A
HOH
308
H
HOH
12
1_555
A
HOH
314
H
HOH
12
14_455
A
HOH
314
H
HOH
12
12_455
97
I 4 2 2