0.022291
0.012870
0.000000
0.000000
0.025740
0.000000
0.000000
0.000000
0.023960
0.00000
0.00000
0.00000
Zhang, W.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
44.861
44.861
41.736
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
C10 H15 N2 O7 P Se
385.169
n
1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one
2-Se-Thymidine-5'-phosphate
DNA 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
P
N
115
N
N
N
116
N
C
N
117
N
SE
N
118
N
N
N
119
N
C
N
120
N
O
N
121
N
C
N
122
N
C
N
123
R
C
N
124
N
O
N
125
N
C
N
126
N
O
N
127
S
C
N
128
N
O
N
129
R
C
N
130
N
O
N
131
N
C
N
132
N
O
N
133
N
C
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
146
N
H
N
147
N
H
N
148
N
H
N
149
N
O
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
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
doub
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
sing
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
doub
To Be Published
0353
DNA 8mer containing two 2SeT modifications
10.2210/pdb5tgp/pdb
pdb_00005tgp
100
1
CCD
2015-10-01
MAR CCD 130 mm
SINGLE WAVELENGTH
M
x-ray
1
0.98
1.0
8.2.1
ALS
0.98
SYNCHROTRON
ALS BEAMLINE 8.2.1
2648.537
DNA/RNA (5'-R(*G)-D(P*(2ST))-R(P*G)-D(P*(2ST))-R(P*AP*CP*AP*C)-3')
2
syn
polymer
18.015
water
25
nat
water
no
yes
G(US3)G(US3)ACAC
GTGTACAC
A,C
polyribonucleotide
n
n
n
n
n
n
n
n
1
2.29
46.26
VAPOR DIFFUSION, HANGING DROP
7.0
10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride, 0.020 M Magnesium chloride hexahydrate
294
-12.200
1
19
A
1
C
8
0.502
A_G1:C8_C
1
-4.682
-0.265
-0.018
-0.087
-10.780
1
20
A
2
C
7
-3.841
A_US32:A7_C
2
-12.192
-0.294
0.126
-0.115
-6.652
1
19
A
3
C
6
0.156
A_G3:C6_C
3
-8.494
-0.168
0.029
-0.140
-2.719
1
20
A
4
C
5
-5.796
A_US34:A5_C
4
-9.800
-0.214
-0.082
-0.109
1.288
1
20
A
5
C
4
-5.229
A_A5:US34_C
5
-8.919
0.359
0.025
-0.076
5.304
1
19
A
6
C
3
-1.985
A_C6:G3_C
6
-9.978
0.249
0.192
-0.165
7.673
1
20
A
7
C
2
-2.550
A_A7:US32_C
7
-12.070
0.154
0.143
-0.172
2.324
1
19
A
8
C
1
-1.937
A_C8:G1_C
8
-0.128
0.212
0.072
-0.192
2.993
33.970
A
A
1
2
8.926
C
C
8
7
3.340
5.194
-0.054
-2.055
AA_G1US32:A7C8_CC
1
1.401
-2.408
33.554
-4.328
0.312
2.448
30.052
A
A
2
3
21.010
C
C
7
6
3.129
10.659
0.360
-1.443
AA_US32G3:C6A7_CC
2
1.960
-3.863
28.072
-4.714
-0.339
2.954
34.007
A
A
3
4
10.965
C
C
6
5
3.266
6.378
-0.819
-1.396
AA_G3US34:A5C6_CC
3
0.123
-0.211
33.421
-3.363
1.419
2.720
33.073
A
A
4
5
17.731
C
C
5
4
3.216
9.945
0.163
-1.200
AA_US34A5:US34A5_CC
4
-0.441
0.786
31.580
-3.670
-0.356
3.068
34.322
A
A
5
6
7.960
C
C
4
3
3.308
4.683
0.614
-1.492
AA_A5C6:G3US34_CC
5
-0.715
1.215
34.004
-3.247
-1.150
2.470
30.068
A
A
6
7
17.467
C
C
3
2
3.084
8.929
0.026
-1.642
AA_C6A7:US32G3_CC
6
-1.131
2.212
28.719
-4.755
-0.252
3.210
35.567
A
A
7
8
6.726
C
C
2
1
3.486
4.098
-0.089
-2.275
AA_A7C8:G1US32_CC
7
-1.826
2.997
35.292
-4.338
-0.127
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Data collection
Database references
Refinement description
1
0
2017-10-18
1
1
2023-10-04
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
N
RCSB
Y
RCSB
2016-09-28
REL
REL
HOH
water
32630
synthetic construct
sample
1
8
1DNS
PDB
experimental model
HOH
23
2
HOH
HOH
101
A
HOH
18
2
HOH
HOH
102
A
HOH
4
2
HOH
HOH
103
A
HOH
22
2
HOH
HOH
104
A
HOH
1
2
HOH
HOH
105
A
HOH
8
2
HOH
HOH
106
A
HOH
3
2
HOH
HOH
107
A
HOH
6
2
HOH
HOH
108
A
HOH
20
2
HOH
HOH
109
A
HOH
9
2
HOH
HOH
110
A
HOH
12
2
HOH
HOH
111
A
HOH
2
2
HOH
HOH
112
A
HOH
21
2
HOH
HOH
113
A
HOH
7
2
HOH
HOH
101
C
HOH
14
2
HOH
HOH
102
C
HOH
17
2
HOH
HOH
103
C
HOH
5
2
HOH
HOH
104
C
HOH
13
2
HOH
HOH
105
C
HOH
10
2
HOH
HOH
106
C
HOH
25
2
HOH
HOH
107
C
HOH
11
2
HOH
HOH
108
C
HOH
16
2
HOH
HOH
109
C
HOH
24
2
HOH
HOH
110
C
HOH
26
2
HOH
HOH
111
C
HOH
15
2
HOH
HOH
112
C
G
1
n
1
G
1
A
2ST
2
n
2
US3
2
A
G
3
n
3
G
3
A
2ST
4
n
4
US3
4
A
A
5
n
5
A
5
A
C
6
n
6
C
6
A
A
7
n
7
A
7
A
C
8
n
8
C
8
A
G
1
n
1
G
1
C
2ST
2
n
2
US3
2
C
G
3
n
3
G
3
C
2ST
4
n
4
US3
4
C
A
5
n
5
A
5
C
C
6
n
6
C
6
C
A
7
n
7
A
7
C
C
8
n
8
C
8
C
author_and_software_defined_assembly
PISA
2
dimeric
780
-0
3080
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
A
O2'
G
1
A
O2'
G
1
1
Y
1
A
O2'
G
3
A
O2'
G
3
1
Y
1
A
O2'
A
5
A
O2'
A
5
1
Y
1
A
O2'
C
6
A
O2'
C
6
1
Y
1
A
O2'
A
7
A
O2'
A
7
1
Y
1
A
O2'
C
8
A
O2'
C
8
1
Y
1
C
O2'
G
1
B
O2'
G
1
1
Y
1
C
O2'
G
3
B
O2'
G
3
1
Y
1
C
O2'
A
5
B
O2'
A
5
1
Y
1
C
O2'
C
6
B
O2'
C
6
1
Y
1
C
O2'
A
7
B
O2'
A
7
1
Y
1
C
O2'
C
8
B
O2'
C
8
1
Y
1
A
A
O5'
O
G
HOH
1
101
2.11
1
14.03
1.20
119.70
133.73
A
A
A
C3'
O3'
P
G
G
US3
1
1
2
Y
1
-18.14
2.20
105.20
87.06
A
A
A
O3'
P
OP2
G
US3
US3
1
2
2
Y
1
-10.68
1.20
119.70
109.02
A
A
A
C3'
O3'
P
US3
US3
G
2
2
3
Y
1
11.97
1.10
110.50
122.47
A
A
A
O3'
P
OP2
US3
G
G
2
3
3
Y
1
7.40
1.20
119.70
127.10
A
A
A
C3'
O3'
P
G
G
US3
3
3
4
Y
1
7.13
1.10
110.50
117.63
A
A
A
O3'
P
OP2
US3
A
A
4
5
5
Y
1
-10.50
0.90
105.70
95.20
A
A
A
O5'
P
OP2
A
A
A
7
7
7
N
1
-7.77
0.90
105.70
97.93
A
A
A
O5'
P
OP1
C
C
C
8
8
8
N
1
13.80
1.20
119.70
133.50
C
C
C
C3'
O3'
P
US3
US3
G
2
2
3
Y
1
-11.80
1.90
104.00
92.20
C
C
C
O3'
P
O5'
US3
G
G
2
3
3
Y
1
12.79
1.20
119.70
132.49
C
C
C
C3'
O3'
P
G
G
US3
3
3
4
Y
1
-23.68
2.20
105.20
81.52
C
C
C
O3'
P
OP1
G
US3
US3
3
4
4
Y
1
A
A
O3'
P
US3
G
2
3
0.095
0.012
1.607
1.702
Y
1
A
A
O3'
P
US3
A
4
5
0.074
0.012
1.607
1.681
Y
1
C
C
O3'
P
G
US3
3
4
-0.161
0.012
1.607
1.446
Y
24.167
0.00
0.00
0.00
0.00
0.00
-0.01
0.969
0.954
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.20811
0.18848
0.18948
1.60
38.85
307
5882
5.0
97.36
1.930
0.065
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.086
0.083
0.80
0.80
1.20
1dns
1.60
38.85
25
347
0
322
0
0.026
0.013
352
0.002
0.020
174
3.505
1.576
520
2.950
3.000
406
0.623
0.200
56
0.024
0.020
184
0.003
0.020
76
2.165
2.527
352
2.167
2.527
351
2.944
3.780
520
3.603
25.908
527
3.530
25.822
516
0.292
0.254
1.643
19
381
20
89.89
1.60
38.85
5TGP
6189
0.788
0.057
1
30.9
6.5
97.1
0.351
1.6
1.66
2.13
1
2.6
92.7
refinement
REFMAC
5.8.0069
data reduction
HKL-2000
1.0
data scaling
HKL-2000
1.0
phasing
PHASER
1.0
N
DNA 8mer containing two 2SeT modifications
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.547
both
A
G
1
A
O3'
G
1
1_555
A
US3
2
A
P
US3
2
1_555
covale
1.702
one
A
US3
2
A
O3'
US3
2
1_555
A
G
3
A
P
G
3
1_555
covale
1.589
both
A
G
3
A
O3'
G
3
1_555
A
US3
4
A
P
US3
4
1_555
covale
1.681
one
A
US3
4
A
O3'
US3
4
1_555
A
A
5
A
P
A
5
1_555
covale
1.675
both
C
G
1
B
O3'
G
1
1_555
C
US3
2
B
P
US3
2
1_555
covale
1.638
one
C
US3
2
B
O3'
US3
2
1_555
C
G
3
B
P
G
3
1_555
covale
1.446
both
C
G
3
B
O3'
G
3
1_555
C
US3
4
B
P
US3
4
1_555
covale
1.595
one
C
US3
4
B
O3'
US3
4
1_555
C
A
5
B
P
A
5
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
C
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
C
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
C
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
US3
2
A
N3
US3
2
1_555
C
A
7
B
N1
A
7
1_555
hydrog
WATSON-CRICK
A
US3
2
A
O4
US3
2
1_555
C
A
7
B
N6
A
7
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
C
C
6
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
C
C
6
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
C
C
6
B
N4
C
6
1_555
hydrog
WATSON-CRICK
A
US3
4
A
N3
US3
4
1_555
C
A
5
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
US3
4
A
O4
US3
4
1_555
C
A
5
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
A
5
A
N1
A
5
1_555
C
US3
4
B
N3
US3
4
1_555
hydrog
WATSON-CRICK
A
A
5
A
N6
A
5
1_555
C
US3
4
B
O4
US3
4
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
C
G
3
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
C
G
3
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
C
G
3
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
A
7
A
N1
A
7
1_555
C
US3
2
B
N3
US3
2
1_555
hydrog
WATSON-CRICK
A
A
7
A
N6
A
7
1_555
C
US3
2
B
O4
US3
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
C
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
C
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
C
G
1
B
N2
G
1
1_555
DNA
DNA, selenium, modification
5TGP
PDB
1
1
5TGP
1
8
5TGP
1
8
5TGP
A
1
1
8
1
8
5TGP
1
8
5TGP
C
1
1
8
169
P 61