0.024033
0.000000
0.000000
0.000000
0.024033
0.000000
0.000000
0.000000
0.041570
0.00000
0.00000
0.00000
Zhang, W.
Sheng, J.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
41.609
41.609
24.056
C11 H17 N2 O8 P Se
415.195
n
5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
DNA linking
Cl -1
35.453
CHLORIDE ION
non-polymer
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
O
N
13
N
C
N
14
N
C
N
15
R
C
N
16
N
C
N
17
R
C
N
18
N
O
N
19
R
C
N
20
R
C
N
21
N
SE
N
22
N
C
N
23
N
O
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
H
N
39
N
H
N
40
N
H
N
41
N
CL
N
42
N
O
N
43
N
P
N
44
N
O
N
45
N
O
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
O
N
50
S
C
N
51
N
O
N
52
N
C
N
53
R
C
Y
54
N
N
Y
55
N
C
Y
56
N
N
Y
57
N
C
Y
58
N
C
N
59
N
N
Y
60
N
N
Y
61
N
C
Y
62
N
N
Y
63
N
C
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
H
N
76
N
H
N
77
N
H
N
78
N
O
N
79
N
P
N
80
N
O
N
81
N
O
N
82
N
O
N
83
N
C
N
84
R
C
N
85
N
O
N
86
S
C
N
87
N
O
N
88
N
C
N
89
R
C
N
90
N
N
N
91
N
C
N
92
N
O
N
93
N
N
N
94
N
C
N
95
N
N
N
96
N
C
N
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
P
N
114
N
O
N
115
N
O
N
116
N
O
N
117
N
C
N
118
R
C
N
119
N
O
N
120
S
C
N
121
N
O
N
122
N
C
N
123
R
C
Y
124
N
N
Y
125
N
C
Y
126
N
N
Y
127
N
C
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
C
N
132
N
N
N
133
N
N
Y
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
148
N
H
N
149
N
O
N
150
N
H
N
151
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
doub
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
doub
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
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
doub
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
Y
65
N
sing
Y
66
N
sing
Y
67
N
doub
N
68
N
sing
Y
69
N
sing
Y
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
73
N
doub
N
74
N
sing
N
75
N
sing
Y
76
N
sing
Y
77
N
doub
N
78
N
sing
Y
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
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
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
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
doub
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
Y
138
N
sing
Y
139
N
sing
Y
140
N
doub
N
141
N
sing
Y
142
N
sing
N
143
N
sing
Y
144
N
doub
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
TO BE PUBLISHED
0353
DNA octamer d(gtggccac) with 2'-se modification
10.2210/pdb4fp6/pdb
pdb_00004fp6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
CCD
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.98
1.0
12.3.1
ALS
0.98
SYNCHROTRON
ALS BEAMLINE 12.3.1
2520.592
DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3')
1
syn
polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
60
nat
water
no
yes
(DG)(2ST)(DG)(DG)(DC)(DC)(DA)(DC)
GTGGCCAC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
2.07
40.45
-19.859
1
19
A
1
A
8
-0.260
A_DG1:DC8_A
1
-6.395
-0.295
-0.350
-0.019
-8.267
1
20
A
2
A
7
0.745
A_2ST2:DA7_A
2
-9.212
-0.082
0.074
-0.133
-2.654
1
19
A
3
A
6
-1.082
A_DG3:DC6_A
3
-10.881
-0.185
0.133
-0.178
-6.885
1
19
A
4
A
5
0.585
A_DG4:DC5_A
4
-16.892
-0.187
-0.056
-0.084
6.885
1
19
A
5
A
4
0.585
A_DC5:DG4_A
5
-16.892
0.187
-0.056
-0.084
2.654
1
19
A
6
A
3
-1.082
A_DC6:DG3_A
6
-10.881
0.185
0.133
-0.178
8.267
1
20
A
7
A
2
0.745
A_DA7:2ST2_A
7
-9.212
0.082
0.074
-0.133
19.859
1
19
A
8
A
1
-0.260
A_DC8:DG1_A
8
-6.395
0.295
-0.350
-0.019
2.657
31.675
A
A
1
2
18.903
A
A
8
7
3.120
10.138
-0.006
-0.963
AA_DG12ST2:DA7DC8_AA
1
-1.947
3.631
29.986
-3.464
-0.315
2.534
30.916
A
A
2
3
17.757
A
A
7
6
3.058
9.325
0.334
-1.316
AA_2ST2DG3:DC6DA7_AA
2
0.062
-0.117
29.509
-4.050
-0.616
2.998
36.392
A
A
3
4
11.695
A
A
6
5
3.341
7.250
0.267
-1.512
AA_DG3DG4:DC5DC6_AA
3
2.932
-4.730
35.569
-3.410
-0.028
2.724
30.257
A
A
4
5
12.487
A
A
5
4
2.943
6.470
0.000
-0.737
AA_DG4DC5:DG4DC5_AA
4
0.000
0.000
29.573
-2.560
0.000
2.998
36.392
A
A
5
6
11.695
A
A
4
3
3.341
7.250
-0.267
-1.512
AA_DC5DC6:DG3DG4_AA
5
-2.932
4.730
35.569
-3.410
0.028
2.534
30.916
A
A
6
7
17.757
A
A
3
2
3.058
9.325
-0.334
-1.316
AA_DC6DA7:2ST2DG3_AA
6
-0.062
0.117
29.509
-4.050
0.616
2.657
31.675
A
A
7
8
18.903
A
A
2
1
3.120
10.138
0.006
-0.963
AA_DA7DC8:DG12ST2_AA
7
1.947
-3.631
29.986
-3.464
0.315
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
1
0
2012-08-15
1
1
2024-02-28
_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
RCSB
Y
RCSB
2012-06-21
REL
REL
CL
CHLORIDE ION
HOH
water
CL
1
2
CL
CL
101
A
HOH
1
3
HOH
HOH
201
A
HOH
2
3
HOH
HOH
202
A
HOH
3
3
HOH
HOH
203
A
HOH
4
3
HOH
HOH
204
A
HOH
5
3
HOH
HOH
205
A
HOH
6
3
HOH
HOH
206
A
HOH
7
3
HOH
HOH
207
A
HOH
8
3
HOH
HOH
208
A
HOH
9
3
HOH
HOH
209
A
HOH
10
3
HOH
HOH
210
A
HOH
11
3
HOH
HOH
211
A
HOH
12
3
HOH
HOH
212
A
HOH
13
3
HOH
HOH
213
A
HOH
14
3
HOH
HOH
214
A
HOH
15
3
HOH
HOH
215
A
HOH
16
3
HOH
HOH
216
A
HOH
17
3
HOH
HOH
217
A
HOH
19
3
HOH
HOH
218
A
HOH
20
3
HOH
HOH
219
A
HOH
22
3
HOH
HOH
220
A
HOH
25
3
HOH
HOH
221
A
HOH
26
3
HOH
HOH
222
A
HOH
27
3
HOH
HOH
223
A
HOH
28
3
HOH
HOH
224
A
HOH
42
3
HOH
HOH
225
A
HOH
44
3
HOH
HOH
226
A
HOH
45
3
HOH
HOH
227
A
HOH
46
3
HOH
HOH
228
A
HOH
47
3
HOH
HOH
229
A
HOH
48
3
HOH
HOH
230
A
HOH
49
3
HOH
HOH
231
A
HOH
50
3
HOH
HOH
232
A
HOH
51
3
HOH
HOH
233
A
HOH
52
3
HOH
HOH
234
A
HOH
53
3
HOH
HOH
235
A
HOH
54
3
HOH
HOH
236
A
HOH
55
3
HOH
HOH
237
A
HOH
56
3
HOH
HOH
238
A
HOH
57
3
HOH
HOH
239
A
HOH
58
3
HOH
HOH
240
A
HOH
63
3
HOH
HOH
241
A
HOH
65
3
HOH
HOH
242
A
HOH
66
3
HOH
HOH
243
A
HOH
67
3
HOH
HOH
244
A
HOH
68
3
HOH
HOH
245
A
HOH
69
3
HOH
HOH
246
A
HOH
74
3
HOH
HOH
247
A
HOH
75
3
HOH
HOH
248
A
HOH
77
3
HOH
HOH
249
A
HOH
78
3
HOH
HOH
250
A
HOH
79
3
HOH
HOH
251
A
HOH
81
3
HOH
HOH
252
A
HOH
82
3
HOH
HOH
253
A
HOH
83
3
HOH
HOH
254
A
HOH
84
3
HOH
HOH
255
A
HOH
85
3
HOH
HOH
256
A
HOH
86
3
HOH
HOH
257
A
HOH
87
3
HOH
HOH
258
A
HOH
88
3
HOH
HOH
259
A
HOH
89
3
HOH
HOH
260
A
G
1
n
1
DG
1
A
2ST
2
n
2
2ST
2
A
G
3
n
3
DG
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
C
6
n
6
DC
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
author_and_software_defined_assembly
PISA
2
dimeric
2240
-14
2820
A
2ST
2
A
2ST
2
DT
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_554
-y,-x,-z-1/2
crystal symmetry operation
0.0000000000
0.0000000000
-12.0280000000
1
A
A
O
O
HOH
HOH
247
248
1.77
1
A
A
O
O
HOH
HOH
209
211
2.18
1
A
DC
8
0.075
SIDE CHAIN
1
-3.02
0.50
128.60
125.58
A
A
A
N3
C4
C5
DG
DG
DG
1
1
1
N
1
-4.74
0.40
104.50
99.76
A
A
A
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
3.33
0.50
104.30
107.63
A
A
A
C5
N7
C8
DG
DG
DG
3
3
3
N
1
-3.11
0.50
113.10
109.99
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-4.05
0.40
104.50
100.45
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
3.65
0.40
110.80
114.45
A
A
A
C4
C5
N7
DG
DG
DG
4
4
4
N
1
-4.87
0.50
104.30
99.43
A
A
A
C5
N7
C8
DG
DG
DG
4
4
4
N
1
-15.12
1.90
104.00
88.88
A
A
A
O3'
P
O5'
DG
DC
DC
4
5
5
Y
1
6.91
1.10
110.50
117.41
A
A
A
O3'
P
OP2
DG
DC
DC
4
5
5
Y
1
-5.82
0.90
105.70
99.88
A
A
A
O5'
P
OP1
DC
DC
DC
5
5
5
N
1
10.16
1.20
110.70
120.86
A
A
A
O5'
P
OP2
DC
DC
DC
5
5
5
N
1
16.29
1.60
120.90
137.19
A
A
A
P
O5'
C5'
DC
DC
DC
5
5
5
N
1
-3.33
0.40
104.50
101.17
A
A
A
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
1
-3.05
0.40
104.50
101.45
A
A
A
O4'
C4'
C3'
DA
DA
DA
7
7
7
N
1
3.69
0.60
118.60
122.29
A
A
A
C6
N1
C2
DA
DA
DA
7
7
7
N
1
4.68
0.40
105.80
110.48
A
A
A
C8
N9
C4
DA
DA
DA
7
7
7
N
1
3.90
0.60
118.60
122.50
A
A
A
N1
C6
N6
DA
DA
DA
7
7
7
N
1
-2.84
0.40
104.50
101.66
A
A
A
O4'
C4'
C3'
DC
DC
DC
8
8
8
N
1
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
4.56
0.40
120.30
124.86
A
A
A
C6
N1
C2
DC
DC
DC
8
8
8
N
1
-5.08
0.70
119.20
114.12
A
A
A
N1
C2
N3
DC
DC
DC
8
8
8
N
1
6.67
0.50
117.40
124.07
A
A
A
C4
C5
C6
DC
DC
DC
8
8
8
N
1
-7.90
0.50
121.00
113.10
A
A
A
C5
C6
N1
DC
DC
DC
8
8
8
N
1
A
A
C4
C5
DG
DG
3
3
-0.042
0.007
1.379
1.337
N
1
A
A
P
OP2
DC
DC
5
5
-0.108
0.017
1.485
1.377
N
1
A
A
O5'
C5'
DC
DC
5
5
-0.189
0.025
1.418
1.229
N
1
A
A
P
OP2
DC
DC
6
6
-0.113
0.017
1.485
1.372
N
1
A
A
N1
C6
DC
DC
6
6
0.040
0.006
1.367
1.407
N
1
A
A
P
O5'
DC
DC
8
8
-0.079
0.010
1.593
1.514
N
1
A
A
N1
C2
DC
DC
8
8
0.093
0.010
1.397
1.490
N
1
A
A
N1
C6
DC
DC
8
8
-0.040
0.006
1.367
1.327
N
1
A
A
N3
C4
DC
DC
8
8
-0.068
0.007
1.335
1.267
N
18.639
0.00
0.00
0.00
0.00
0.00
0.00
0.966
0.955
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.22110
0.18967
0.19101
1.28
29.42
263
5489
4.6
98.59
0.977
0.041
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.055
0.058
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
1.28
29.42
60
224
1
163
0
0.039
0.021
180
3.521
3.000
271
0.435
0.200
32
0.040
0.020
84
2.306
3.000
180
2.580
4.500
271
0.337
0.357
1.311
17
366
20
89.70
1.28
29.42
4FP6
5489
5890
1
refinement
REFMAC
5.5.0110
DNA octamer d(gtggccac) with 2'-se modification
1
N
N
2
N
N
3
N
N
covale
1.644
both
A
DG
1
A
O3'
DG
1
1_555
A
2ST
2
A
P
2ST
2
1_555
covale
1.661
both
A
2ST
2
A
O3'
2ST
2
1_555
A
DG
3
A
P
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
8
A
N3
DC
8
8_554
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
8
A
O2
DC
8
8_554
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
8_554
hydrog
WATSON-CRICK
A
2ST
2
A
N3
2ST
2
1_555
A
DA
7
A
N1
DA
7
8_554
hydrog
WATSON-CRICK
A
2ST
2
A
O4
2ST
2
1_555
A
DA
7
A
N6
DA
7
8_554
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
DC
6
A
N3
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
DC
6
A
O2
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
DC
6
A
N4
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
5
A
N3
DC
5
8_554
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
5
A
O2
DC
5
8_554
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
5
A
N4
DC
5
8_554
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
4
A
N1
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
4
A
O6
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
4
A
N2
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
3
A
N1
DG
3
8_554
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
3
A
O6
DG
3
8_554
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
3
A
N2
DG
3
8_554
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
A
2ST
2
A
N3
2ST
2
8_554
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
A
2ST
2
A
O4
2ST
2
8_554
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
A
DG
1
A
N1
DG
1
8_554
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
8_554
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
A
DG
1
A
N2
DG
1
8_554
DNA
2'-SE-THYMIDINE DNA, DNA
4FP6
PDB
1
4FP6
1
8
4FP6
1
8
4FP6
A
1
1
8
BINDING SITE FOR RESIDUE CL A 101
A
CL
101
Software
7
A
HOH
205
C
HOH
7
8_554
A
HOH
216
C
HOH
7
1_555
A
HOH
216
C
HOH
7
8_554
A
HOH
226
C
HOH
7
8_554
A
HOH
247
C
HOH
7
8_554
A
HOH
248
C
HOH
7
8_554
A
HOH
248
C
HOH
7
1_555
96
P 43 21 2