0.038850
-0.000000
0.000000
0.000000
0.009383
0.000000
0.000000
0.000000
0.033047
0.00000
0.00000
0.00000
Shi, K.
Pan, B.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
25.740
106.580
30.260
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
Na 1
22.990
SODIUM 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
O
N
112
N
H
N
113
N
H
N
114
N
NA
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
Nucleic Acids Res.
NARHAD
0389
0305-1048
31
1392
1397
10.1093/nar/gkg226
12595546
The crystal structure of an alternating RNA heptamer r(GUAUACA)
forming a six base-paired duplex with 3'-end adenine overhangs
2003
10.2210/pdb1l3z/pdb
pdb_00001l3z
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
IMAGE PLATE
RIGAKU
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
2205.379
5'-R(*GP*UP*AP*UP*AP*CP*A)-3'
2
syn
polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
39
nat
water
no
no
GUAUACA
GUAUACA
A,B
polyribonucleotide
n
n
n
n
n
n
n
1
2.35
47.72
7.0
MPD, CaCl2, Cacodylate buffer, pH7.0
MPD
1
CaCl2
1
Cacodylate buffer
1
-5.969
1
19
B
8
B
13
-0.483
B_G8:C13_B
1
-11.701
-0.203
0.112
-0.138
-2.264
1
20
B
9
B
12
0.967
B_U9:A12_B
2
-11.661
-0.223
0.271
-0.130
1.192
1
20
B
10
B
11
6.990
B_A10:U11_B
3
-15.805
-0.059
0.260
-0.119
-1.192
1
20
B
11
B
10
6.990
B_U11:A10_B
4
-15.805
0.059
0.260
-0.119
2.264
1
20
B
12
B
9
0.967
B_A12:U9_B
5
-11.661
0.223
0.271
-0.130
5.969
1
19
B
13
B
8
-0.483
B_C13:G8_B
6
-11.701
0.203
0.112
-0.138
2.769
32.045
B
B
8
9
13.922
B
B
13
12
3.186
7.603
-0.116
-1.405
BB_G8U9:A12C13_BB
1
-3.294
6.032
30.983
-3.814
-0.340
2.258
34.365
B
B
9
10
23.663
B
B
12
11
3.072
13.619
0.115
-1.490
BB_U9A10:U11A12_BB
2
0.179
-0.310
31.626
-4.335
-0.171
2.664
34.009
B
B
10
11
21.796
B
B
11
10
3.300
12.467
0.000
-1.173
BB_A10U11:A10U11_BB
3
0.000
0.000
31.704
-3.888
0.000
2.258
34.365
B
B
11
12
23.663
B
B
10
9
3.072
13.619
-0.115
-1.490
BB_U11A12:U9A10_BB
4
-0.179
0.310
31.626
-4.335
0.171
2.769
32.045
B
B
12
13
13.922
B
B
9
8
3.186
7.603
0.116
-1.405
BB_A12C13:G8U9_BB
5
3.294
-6.032
30.983
-3.814
0.340
software
diffrn_source
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Data collection
Database references
Derived calculations
1
0
2003-02-25
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-10-11
1
4
2018-03-07
1
5
2024-02-14
_diffrn_source.source
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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_symmetry
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_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
2002-03-04
REL
REL
NA
SODIUM ION
HOH
water
NA
301
2
NA
NA
301
A
WAT
101
3
HOH
HOH
101
A
WAT
102
3
HOH
HOH
102
A
WAT
104
3
HOH
HOH
104
A
WAT
105
3
HOH
HOH
105
A
WAT
106
3
HOH
HOH
106
A
WAT
107
3
HOH
HOH
107
A
WAT
108
3
HOH
HOH
108
A
WAT
119
3
HOH
HOH
119
A
WAT
120
3
HOH
HOH
120
A
WAT
121
3
HOH
HOH
121
A
WAT
122
3
HOH
HOH
122
A
WAT
123
3
HOH
HOH
123
A
WAT
125
3
HOH
HOH
125
A
WAT
126
3
HOH
HOH
126
A
WAT
127
3
HOH
HOH
127
A
WAT
128
3
HOH
HOH
128
A
WAT
129
3
HOH
HOH
129
A
WAT
132
3
HOH
HOH
132
A
WAT
136
3
HOH
HOH
136
A
WAT
137
3
HOH
HOH
137
A
WAT
138
3
HOH
HOH
138
A
WAT
202
3
HOH
HOH
202
A
WAT
103
3
HOH
HOH
103
B
WAT
109
3
HOH
HOH
109
B
WAT
110
3
HOH
HOH
110
B
WAT
111
3
HOH
HOH
111
B
WAT
112
3
HOH
HOH
112
B
WAT
113
3
HOH
HOH
113
B
WAT
114
3
HOH
HOH
114
B
WAT
115
3
HOH
HOH
115
B
WAT
116
3
HOH
HOH
116
B
WAT
117
3
HOH
HOH
117
B
WAT
118
3
HOH
HOH
118
B
WAT
124
3
HOH
HOH
124
B
WAT
130
3
HOH
HOH
130
B
WAT
133
3
HOH
HOH
133
B
WAT
134
3
HOH
HOH
134
B
WAT
135
3
HOH
HOH
135
B
WAT
201
3
HOH
HOH
201
B
GUA
1
n
1
G
1
A
URI
2
n
2
U
2
A
ADE
3
n
3
A
3
A
URI
4
n
4
U
4
A
ADE
5
n
5
A
5
A
CYT
6
n
6
C
6
A
ADE
7
n
7
A
7
A
GUA
8
n
1
G
8
B
URI
9
n
2
U
9
B
ADE
10
n
3
A
10
B
URI
11
n
4
U
11
B
ADE
12
n
5
A
12
B
CYT
13
n
6
C
13
B
ADE
14
n
7
A
14
B
author_defined_assembly
2
dimeric
author_defined_assembly
2
dimeric
A
HOH
202
D
O
HOH
1_555
A
NA
301
C
NA
NA
1_555
A
HOH
202
D
O
HOH
6_555
1.5
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
3_555
-x,y,-z
crystal symmetry 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
3_556
-x,y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
30.2600000000
1
A
NA
301
C
NA
1
A
HOH
129
D
HOH
1
A
HOH
202
D
HOH
1
B
HOH
201
E
HOH
30.5
3.28
0.00
0.00
-2.95
0.00
-0.34
0.225
0.014
0.18
0.18
2.01
20.00
259
2808
9.2
92.5
RANDOM
545644.27
1
RESTRAINED
THROUGHOUT
2.0
0.24
0.21
5.00
0.24
0.23
2.01
20.00
39
332
1
292
0
0.003
0.8
10.5
1.33
1.52
1.50
2.12
2.00
1.33
2.00
1.85
2.50
0.289
0.049
0.245
2.13
35
329
6
9.6
74.0
18.1
2.01
50.0
1L3Z
22206
0
1
93.8
2.01
2.13
data scaling
SCALEPACK
phasing
AMoRE
refinement
CNS
Crystal Structure Analysis of an RNA Heptamer
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
metalc
2.347
A
HOH
202
D
O
HOH
1_555
A
NA
301
C
NA
NA
1_555
metalc
2.347
A
HOH
202
D
O
HOH
6_555
A
NA
301
C
NA
NA
1_555
hydrog
WATSON-CRICK
B
G
8
B
N1
G
1
1_555
B
C
13
B
N3
C
6
3_556
hydrog
WATSON-CRICK
B
G
8
B
N2
G
1
1_555
B
C
13
B
O2
C
6
3_556
hydrog
WATSON-CRICK
B
G
8
B
O6
G
1
1_555
B
C
13
B
N4
C
6
3_556
hydrog
WATSON-CRICK
B
U
9
B
N3
U
2
1_555
B
A
12
B
N1
A
5
3_556
hydrog
WATSON-CRICK
B
U
9
B
O4
U
2
1_555
B
A
12
B
N6
A
5
3_556
hydrog
WATSON-CRICK
B
A
10
B
N1
A
3
1_555
B
U
11
B
N3
U
4
3_556
hydrog
WATSON-CRICK
B
A
10
B
N6
A
3
1_555
B
U
11
B
O4
U
4
3_556
hydrog
WATSON-CRICK
B
U
11
B
N3
U
4
1_555
B
A
10
B
N1
A
3
3_556
hydrog
WATSON-CRICK
B
U
11
B
O4
U
4
1_555
B
A
10
B
N6
A
3
3_556
hydrog
WATSON-CRICK
B
A
12
B
N1
A
5
1_555
B
U
9
B
N3
U
2
3_556
hydrog
WATSON-CRICK
B
A
12
B
N6
A
5
1_555
B
U
9
B
O4
U
2
3_556
hydrog
WATSON-CRICK
B
C
13
B
N3
C
6
1_555
B
G
8
B
N1
G
1
3_556
hydrog
WATSON-CRICK
B
C
13
B
N4
C
6
1_555
B
G
8
B
O6
G
1
3_556
hydrog
WATSON-CRICK
B
C
13
B
O2
C
6
1_555
B
G
8
B
N2
G
1
3_556
RNA
RNA
1L3Z
PDB
1
1L3Z
1
7
1L3Z
1
7
1L3Z
A
1
1
7
8
14
1L3Z
8
14
1L3Z
B
1
1
7
BINDING SITE FOR RESIDUE NA A 301
A
NA
301
Software
6
A
HOH
125
D
HOH
6
6_555
A
HOH
125
D
HOH
6
1_555
A
HOH
127
D
HOH
6
6_555
A
HOH
127
D
HOH
6
1_555
A
HOH
202
D
HOH
6
6_555
A
HOH
202
D
HOH
6
1_555
21
C 2 2 2