0.037902
0.000000
0.000000
-0.000000
0.027193
0.000000
0.000000
-0.000000
0.012878
0.00000
0.00000
0.00000
Kowal, E.A.
Lad, R.
Pallan, P.S.
Muffly, E.
Wawrzak, Z.
Egli, M.
Sturla, S.J.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
26.384
36.774
77.653
C17 H20 N5 O7 P
437.344
6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE
O6-BENZYL-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C16 H17 N2 O7 P
380.289
1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one
DNA linking
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
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
C10 H26 N4
202.340
SPERMINE
non-polymer
Sr 2
87.620
STRONTIUM ION
non-polymer
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
Y
5
N
C
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
Y
10
N
C
N
11
N
C
N
12
N
O
Y
13
N
C
Y
14
N
N
Y
15
N
C
N
16
N
N
Y
17
N
N
Y
18
N
C
Y
19
N
C
Y
20
N
N
Y
21
N
C
Y
22
N
N
N
23
R
C
N
24
N
O
N
25
N
C
N
26
N
C
N
27
R
C
N
28
S
C
N
29
N
O
N
30
N
O
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
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
O
N
52
N
P
N
53
N
O
N
54
N
O
N
55
N
C
N
56
R
C
N
57
N
O
N
58
S
C
N
59
N
O
N
60
N
C
N
61
R
C
N
62
N
N
N
63
N
C
N
64
N
O
N
65
N
N
Y
66
N
C
Y
67
N
C
Y
68
N
C
Y
69
N
C
Y
70
N
C
Y
71
N
C
Y
72
N
C
Y
73
N
C
Y
74
N
C
Y
75
N
C
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
O
N
93
N
H
N
94
N
O
N
95
N
P
N
96
N
O
N
97
N
O
N
98
N
O
N
99
N
C
N
100
R
C
N
101
N
O
N
102
S
C
N
103
N
O
N
104
N
C
N
105
R
C
Y
106
N
N
Y
107
N
C
Y
108
N
N
Y
109
N
C
Y
110
N
C
N
111
N
N
Y
112
N
N
Y
113
N
C
Y
114
N
N
Y
115
N
C
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
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
O
N
131
N
P
N
132
N
O
N
133
N
O
N
134
N
O
N
135
N
C
N
136
R
C
N
137
N
O
N
138
S
C
N
139
N
O
N
140
N
C
N
141
R
C
N
142
N
N
N
143
N
C
N
144
N
O
N
145
N
N
N
146
N
C
N
147
N
N
N
148
N
C
N
149
N
C
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
O
N
165
N
P
N
166
N
O
N
167
N
O
N
168
N
O
N
169
N
C
N
170
R
C
N
171
N
O
N
172
S
C
N
173
N
O
N
174
N
C
N
175
R
C
Y
176
N
N
Y
177
N
C
Y
178
N
N
Y
179
N
C
N
180
N
C
N
181
N
O
N
182
N
N
N
183
N
C
N
184
N
N
N
185
N
N
Y
186
N
C
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
O
N
202
N
P
N
203
N
O
N
204
N
O
N
205
N
O
N
206
N
C
N
207
R
C
N
208
N
O
N
209
S
C
N
210
N
O
N
211
N
C
N
212
R
C
N
213
N
N
N
214
N
C
N
215
N
O
N
216
N
N
N
217
N
C
N
218
N
O
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
O
N
238
N
H
N
239
N
H
N
240
N
N
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
N
N
245
N
C
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
N
N
250
N
C
N
251
N
C
N
252
N
C
N
253
N
N
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
SR
N
1
N
sing
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
Y
7
N
sing
Y
8
N
doub
N
9
N
sing
Y
10
N
doub
N
11
N
sing
Y
12
N
sing
N
13
N
sing
Y
14
N
doub
N
15
N
sing
Y
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
Y
23
N
sing
Y
24
N
doub
Y
25
N
doub
N
26
N
sing
Y
27
N
sing
N
28
N
sing
N
29
N
sing
Y
30
N
doub
Y
31
N
sing
Y
32
N
sing
Y
33
N
sing
Y
34
N
doub
Y
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
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
doub
N
61
N
sing
N
62
N
sing
N
63
N
sing
Y
64
N
doub
Y
65
N
sing
Y
66
N
sing
N
67
N
sing
N
68
N
sing
Y
69
N
doub
N
70
N
sing
Y
71
N
doub
Y
72
N
sing
Y
73
N
sing
Y
74
N
sing
Y
75
N
doub
Y
76
N
doub
N
77
N
sing
Y
78
N
sing
N
79
N
sing
N
80
N
doub
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
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
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
sing
Y
123
N
sing
Y
124
N
sing
Y
125
N
doub
N
126
N
sing
Y
127
N
sing
Y
128
N
sing
Y
129
N
doub
N
130
N
sing
Y
131
N
doub
N
132
N
sing
N
133
N
sing
Y
134
N
sing
Y
135
N
doub
N
136
N
sing
Y
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
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
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
doub
N
164
N
sing
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
doub
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
Y
196
N
sing
Y
197
N
sing
Y
198
N
doub
N
199
N
sing
Y
200
N
sing
N
201
N
sing
Y
202
N
doub
N
203
N
doub
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
doub
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
doub
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
doub
N
242
N
sing
N
243
N
sing
N
244
N
doub
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
41
7566
7576
10.1093/nar/gkt488
23748954
Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.
2013
10.2210/pdb4hqi/pdb
pdb_00004hqi
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
100
2
Si(111)
CCD
2009-07-17
MARMOSAIC 300 mm CCD
C(111)
CCD
2008-07-18
MARMOSAIC 300 mm CCD
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
C(111)
SINGLE WAVELENGTH
M
x-ray
1
1.60499
1.0
0.97857
1.0
21-ID-D
APS
1.60499
SYNCHROTRON
APS BEAMLINE 21-ID-D
21-ID-G
APS
0.97857
SYNCHROTRON
APS BEAMLINE 21-ID-G
3826.607
Short modified nucleic acids
2
syn
polymer
202.340
SPERMINE
1
syn
non-polymer
87.620
STRONTIUM ION
1
syn
non-polymer
18.015
water
49
nat
water
no
yes
(DC)(DG)(DC)(BZG)(DA)(DA)(DT)(DT)(D3N)(DG)(DC)(DG)
CGCNAATTXGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2
2.46
50.02
VAPOR DIFFUSION, HANGING DROP
7.0
20 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 20 mM LiCl, 40 mM SrCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
VAPOR DIFFUSION, HANGING DROP
7.0
20 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 40 mM KCl, 10 mM BaCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
-11.324
1
19
A
2
B
23
-1.868
A_DG2:DC23_B
1
3.168
-0.125
-0.220
-0.253
2.151
1
19
A
3
B
22
-1.099
A_DC3:DG22_B
2
10.773
0.199
-0.317
-0.225
-12.406
1
20
A
5
B
20
1.251
A_DA5:DT20_B
3
0.879
-0.236
-0.460
-0.008
-5.111
1
20
A
6
B
19
0.172
A_DA6:DT19_B
4
-11.621
-0.009
-0.125
-0.142
2.516
1
20
A
7
B
18
1.351
A_DT7:DA18_B
5
-6.703
0.132
-0.126
-0.121
8.065
1
20
A
8
B
17
4.832
A_DT8:DA17_B
6
-0.035
0.024
-0.510
-0.181
-0.234
1
19
A
10
B
15
0.472
A_DG10:DC15_B
7
8.429
-0.259
-0.143
-0.158
10.713
1
19
A
11
B
14
-1.590
A_DC11:DG14_B
8
2.217
0.194
-0.063
-0.224
2.973
30.542
A
A
2
3
-4.943
B
B
23
22
3.016
-2.600
0.825
-0.036
AA_DG2DC3:DG22DC23_BB
1
-1.267
2.408
30.408
0.405
-1.796
3.072
28.292
A
A
5
6
18.000
B
B
20
19
3.259
8.650
-0.057
-0.095
AA_DA5DA6:DT19DT20_BB
2
-2.570
5.348
26.842
-2.189
-0.476
2.933
28.384
A
A
6
7
12.755
B
B
19
18
3.135
6.206
-0.148
-0.601
AA_DA6DT7:DA18DT19_BB
3
0.082
-0.169
27.711
-2.567
0.320
3.374
34.418
A
A
7
8
13.696
B
B
18
17
3.235
7.993
1.209
0.289
AA_DT7DT8:DA17DA18_BB
4
6.047
-10.360
32.969
-0.800
-1.070
3.110
30.984
A
A
10
11
-5.470
B
B
15
14
3.141
-2.918
-0.894
0.014
AA_DG10DC11:DG14DC15_BB
5
0.568
-1.064
30.844
0.565
1.778
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_conn_type
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
1
0
2013-07-10
1
1
2013-09-11
1
2
2024-02-28
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_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_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_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_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-10-25
REL
REL
SPM
SPERMINE
SR
STRONTIUM ION
HOH
water
Chemically synthesized modified oligonucleotides
32630
SYNTHETIC CONSTRUCT
sample
SPM
330
2
SPM
SPM
101
A
SR
1
3
SR
SR
102
A
HOH
4
4
HOH
HOH
201
A
HOH
7
4
HOH
HOH
202
A
HOH
11
4
HOH
HOH
203
A
HOH
12
4
HOH
HOH
204
A
HOH
13
4
HOH
HOH
205
A
HOH
19
4
HOH
HOH
206
A
HOH
20
4
HOH
HOH
207
A
HOH
21
4
HOH
HOH
208
A
HOH
22
4
HOH
HOH
209
A
HOH
23
4
HOH
HOH
210
A
HOH
24
4
HOH
HOH
211
A
HOH
25
4
HOH
HOH
212
A
HOH
26
4
HOH
HOH
213
A
HOH
28
4
HOH
HOH
214
A
HOH
30
4
HOH
HOH
215
A
HOH
31
4
HOH
HOH
216
A
HOH
32
4
HOH
HOH
217
A
HOH
33
4
HOH
HOH
218
A
HOH
34
4
HOH
HOH
219
A
HOH
35
4
HOH
HOH
220
A
HOH
37
4
HOH
HOH
221
A
HOH
38
4
HOH
HOH
222
A
HOH
39
4
HOH
HOH
223
A
HOH
41
4
HOH
HOH
224
A
HOH
44
4
HOH
HOH
225
A
HOH
48
4
HOH
HOH
226
A
HOH
49
4
HOH
HOH
227
A
HOH
50
4
HOH
HOH
228
A
HOH
2
4
HOH
HOH
101
B
HOH
3
4
HOH
HOH
102
B
HOH
5
4
HOH
HOH
103
B
HOH
6
4
HOH
HOH
104
B
HOH
8
4
HOH
HOH
105
B
HOH
9
4
HOH
HOH
106
B
HOH
10
4
HOH
HOH
107
B
HOH
14
4
HOH
HOH
108
B
HOH
15
4
HOH
HOH
109
B
HOH
16
4
HOH
HOH
110
B
HOH
17
4
HOH
HOH
111
B
HOH
18
4
HOH
HOH
112
B
HOH
27
4
HOH
HOH
113
B
HOH
29
4
HOH
HOH
114
B
HOH
36
4
HOH
HOH
115
B
HOH
40
4
HOH
HOH
116
B
HOH
42
4
HOH
HOH
117
B
HOH
43
4
HOH
HOH
118
B
HOH
45
4
HOH
HOH
119
B
HOH
46
4
HOH
HOH
120
B
HOH
47
4
HOH
HOH
121
B
n
1
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
3
A
BZG
4
n
4
BZG
4
A
DA
5
n
5
DA
5
A
DA
6
n
6
DA
6
A
DT
7
n
7
DT
7
A
DT
8
n
8
DT
8
A
D3N
9
n
9
D3N
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DG
12
n
12
DG
12
A
DC
13
n
1
DC
13
B
DG
14
n
2
DG
14
B
DC
15
n
3
DC
15
B
BZG
16
n
4
BZG
16
B
DA
17
n
5
DA
17
B
DA
18
n
6
DA
18
B
DT
19
n
7
DT
19
B
DT
20
n
8
DT
20
B
D3N
21
n
9
D3N
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
24
n
12
DG
24
B
author_and_software_defined_assembly
PISA
2
dimeric
1890
-24
4860
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
B
O5'
DC
13
B
O5'
DC
1
1
Y
1
B
C5'
DC
13
B
C5'
DC
1
1
Y
1
B
C4'
DC
13
B
C4'
DC
1
1
Y
1
B
O4'
DC
13
B
O4'
DC
1
1
Y
1
B
C3'
DC
13
B
C3'
DC
1
1
Y
1
B
C2'
DC
13
B
C2'
DC
1
1
Y
1
B
C1'
DC
13
B
C1'
DC
1
1
Y
1
B
N1
DC
13
B
N1
DC
1
1
Y
1
B
C2
DC
13
B
C2
DC
1
1
Y
1
B
O2
DC
13
B
O2
DC
1
1
Y
1
B
N3
DC
13
B
N3
DC
1
1
Y
1
B
C4
DC
13
B
C4
DC
1
1
Y
1
B
N4
DC
13
B
N4
DC
1
1
Y
1
B
C5
DC
13
B
C5
DC
1
1
Y
1
B
C6
DC
13
B
C6
DC
1
1
Y
1
A
DC
1
A
DC
1
1
Y
1
A
A
O
O
HOH
HOH
225
226
2.09
1
B
B
O
O
HOH
HOH
103
104
2.19
1
-6.22
1.00
110.10
103.88
A
A
A
C1'
O4'
C4'
DC
DC
DC
3
3
3
N
44.140
3.33
-0.00
-0.00
1.38
0.00
-4.71
0.954
0.940
0.29823
0.25885
0.26227
1.70
20.67
734
7486
8.9
93.39
4.224
0.130
RANDOM
1,2
THROUGHOUT
SAD
0.149
0.144
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.70
20.67
49
545
15
481
0
0.011
0.013
554
1.652
1.578
833
0.125
0.200
66
0.023
0.020
260
0.336
0.336
1.745
36
338
20
57.01
1.70
30.0
4HQI
8811
8236
5
0.044
1,2
52.33
6.4
93.4
0.228
1.70
1.76
5.65
524
1,2
4
data collection
MD2
diffractometer software from EMBL (with LS-CAT developed extensions)
model building
PHENIX
refinement
REFMAC
5.7.0029
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
covale
1.586
both
A
DC
3
A
O3'
DC
3
1_555
A
BZG
4
A
P
BZG
4
1_555
covale
1.578
both
A
DT
8
A
O3'
DT
8
1_555
A
D3N
9
A
P
D3N
9
1_555
covale
1.595
both
B
DC
15
B
O3'
DC
3
1_555
B
BZG
16
B
P
BZG
4
1_555
covale
1.591
both
B
DT
20
B
O3'
DT
8
1_555
B
D3N
21
B
P
D3N
9
1_555
metalc
2.690
A
DG
12
A
O6
DG
12
1_555
A
SR
102
D
SR
SR
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
19
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
19
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
DNA
B-form DNA, O6-Benzyl-2'-deoxyguanosine, dPer, Perimidinone-Derived Nucleoside, Dickerson-Drew Dodecamer, DNA
4HQI
PDB
1
4HQI
1
12
4HQI
1
12
4HQI
A
1
1
12
13
24
4HQI
13
24
4HQI
B
1
1
12
BINDING SITE FOR RESIDUE SPM A 101
A
SPM
101
Software
6
BINDING SITE FOR RESIDUE SR A 102
A
SR
102
Software
1
A
DG
2
A
DG
2
6
1_555
A
D3N
9
A
D3N
9
6
2_555
A
D3N
9
A
D3N
9
6
3_645
A
DG
10
A
DG
10
6
2_555
B
DG
14
B
DG
2
6
2_555
B
DG
22
B
DG
10
6
1_555
A
DG
12
A
DG
12
1
1_555
19
P 21 21 21