1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hoehn, S.T.
Junker, H.-D.
Bunt, R.C.
Turner, C.J.
Stubbe, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
Co 3
58.933
COBALT (III) ION
non-polymer
C55 H85 N20 O21 S2 1
1426.515
BLEOMYCIN B2
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
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
O
15.999
OXYGEN ATOM
non-polymer
H2 O2
34.015
HYDROGEN PEROXIDE
non-polymer
C2 H5 O6 P
156.031
2-PHOSPHOGLYCOLIC ACID
non-polymer
N
1
N
CO
N
2
N
N
N
3
S
C
N
4
N
C
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
N
N
9
N
N
N
10
N
C
N
11
N
C
N
12
N
O
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
N
N
19
S
C
N
20
N
N
N
21
N
C
N
22
N
C
N
23
N
O
N
24
N
N
N
25
S
C
N
26
N
C
N
27
N
O
N
28
R
C
Y
29
N
C
N
30
N
O
Y
31
N
N
Y
32
N
C
Y
33
N
C
Y
34
N
N
N
35
N
N
N
36
S
C
N
37
N
C
N
38
N
O
N
39
N
O
N
40
R
C
N
41
N
C
N
42
S
C
N
43
N
C
N
44
N
N
N
45
S
C
N
46
N
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
N
C
N
51
N
N
N
52
N
C
N
53
N
C
N
54
N
O
Y
55
N
C
N
56
N
C
Y
57
N
S
Y
58
N
C
Y
59
N
C
Y
60
N
N
Y
61
N
C
Y
62
N
C
Y
63
N
N
Y
64
N
C
Y
65
N
S
N
66
N
N
N
67
N
C
N
68
N
C
N
69
N
C
N
70
N
C
N
71
N
C
N
72
N
N
N
73
N
N
N
74
N
N
N
75
N
O
N
76
N
O
N
77
N
C
N
78
N
O
N
79
N
O
N
80
S
C
N
81
N
O
N
82
R
C
N
83
S
C
N
84
S
C
N
85
S
C
N
86
S
C
N
87
S
C
N
88
R
C
N
89
R
C
N
90
N
O
N
91
R
C
N
92
N
O
N
93
N
O
N
94
N
O
N
95
N
N
N
96
N
C
N
97
N
O
N
98
N
O
N
99
N
C
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
H
N
114
N
H
N
115
N
H
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
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
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
H
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
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
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
O
N
186
N
P
N
187
N
O
N
188
N
O
N
189
N
O
N
190
N
C
N
191
R
C
N
192
N
O
N
193
S
C
N
194
N
O
N
195
N
C
N
196
R
C
Y
197
N
N
Y
198
N
C
Y
199
N
N
Y
200
N
C
Y
201
N
C
N
202
N
N
Y
203
N
N
Y
204
N
C
Y
205
N
N
Y
206
N
C
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
O
N
222
N
P
N
223
N
O
N
224
N
O
N
225
N
O
N
226
N
C
N
227
R
C
N
228
N
O
N
229
S
C
N
230
N
O
N
231
N
C
N
232
R
C
N
233
N
N
N
234
N
C
N
235
N
O
N
236
N
N
N
237
N
C
N
238
N
N
N
239
N
C
N
240
N
C
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
O
N
256
N
P
N
257
N
O
N
258
N
O
N
259
N
O
N
260
N
C
N
261
R
C
N
262
N
O
N
263
S
C
N
264
N
O
N
265
N
C
N
266
R
C
Y
267
N
N
Y
268
N
C
Y
269
N
N
Y
270
N
C
N
271
N
C
N
272
N
O
N
273
N
N
N
274
N
C
N
275
N
N
N
276
N
N
Y
277
N
C
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
O
N
293
N
P
N
294
N
O
N
295
N
O
N
296
N
O
N
297
N
C
N
298
R
C
N
299
N
O
N
300
S
C
N
301
N
O
N
302
N
C
N
303
R
C
N
304
N
N
N
305
N
C
N
306
N
O
N
307
N
N
N
308
N
C
N
309
N
O
N
310
N
C
N
311
N
C
N
312
N
C
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
O
N
329
N
O
N
330
N
O
N
331
N
H
N
332
N
H
N
333
N
P
N
334
N
O
N
335
N
O
N
336
N
O
N
337
N
O
N
338
N
C
N
339
N
C
N
340
N
O
N
341
N
O
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
doub
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
doub
Y
24
N
doub
Y
25
N
sing
N
26
N
sing
Y
27
N
sing
N
28
N
sing
Y
29
N
doub
N
30
N
sing
Y
31
N
sing
Y
32
N
doub
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
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
doub
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
Y
52
N
sing
Y
53
N
doub
N
54
N
sing
Y
55
N
doub
Y
56
N
sing
N
57
N
sing
Y
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
sing
N
67
N
doub
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
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
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
doub
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
doub
N
102
N
sing
N
103
N
sing
Y
104
N
sing
Y
105
N
doub
N
106
N
sing
N
107
N
sing
Y
108
N
sing
Y
109
N
doub
N
110
N
sing
Y
111
N
sing
Y
112
N
sing
Y
113
N
doub
Y
114
N
sing
N
115
N
sing
Y
116
N
sing
Y
117
N
doub
Y
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
doub
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
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
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
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
doub
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
doub
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
Y
212
N
sing
Y
213
N
sing
Y
214
N
doub
N
215
N
sing
Y
216
N
sing
Y
217
N
sing
Y
218
N
doub
N
219
N
sing
Y
220
N
doub
N
221
N
sing
N
222
N
sing
Y
223
N
sing
Y
224
N
doub
N
225
N
sing
Y
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
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
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
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
doub
N
253
N
sing
N
254
N
doub
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
doub
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
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
Y
285
N
sing
Y
286
N
sing
Y
287
N
doub
N
288
N
sing
Y
289
N
sing
N
290
N
sing
Y
291
N
doub
N
292
N
doub
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
doub
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
doub
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
N
331
N
sing
N
332
N
sing
N
333
N
doub
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
doub
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
353
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
40
5894
5905
10.1021/bi002635g
11352724
Solution structure of Co(III)-bleomycin-OOH bound to a phosphoglycolate lesion containing oligonucleotide: implications for bleomycin-induced double-strand DNA cleavage.
2001
10.2210/pdb1gj2/pdb
pdb_00001gj2
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1802.232
5'-D(*CP*CP*AP*AP*AP*G)-3'
1
syn
polymer
1849.241
5'-D(P*AP*CP*TP*GP*GP*G)-3'
1
syn
polymer
3942.572
5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
1
syn
polymer
156.031
2-PHOSPHOGLYCOLIC ACID
1
man
non-polymer
58.933
COBALT (III) ION
1
syn
non-polymer
15.999
OXYGEN ATOM
1
syn
non-polymer
1426.515
BLEOMYCIN B2
1
syn
non-polymer
34.015
HYDROGEN PEROXIDE
1
syn
non-polymer
no
no
(DC)(DC)(DA)(DA)(DA)(DG)
CCAAAG
A
polydeoxyribonucleotide
no
no
(DA)(DC)(DT)(DG)(DG)(DG)
ACTGGG
B
polydeoxyribonucleotide
no
no
(DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG)
CCCAGTACTTTGG
C
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
20.382
1
19
A
1
C
26
-3.249
A_DC1:DG26_C
1
-23.335
0.393
-0.260
-0.239
3.758
1
19
A
2
C
25
-5.198
A_DC2:DG25_C
2
-9.799
0.575
-0.005
-0.381
2.825
1
20
A
3
C
24
7.227
A_DA3:DT24_C
3
7.265
-0.309
0.522
-0.289
-2.675
1
20
A
4
C
23
0.058
A_DA4:DT23_C
4
3.099
0.009
0.468
-0.299
4.559
1
20
A
5
C
22
-0.471
A_DA5:DT22_C
5
0.743
-0.305
0.380
-0.304
9.925
1
19
A
6
C
21
-4.746
A_DG6:DC21_C
6
4.080
-0.487
0.650
-0.367
-1.203
1
20
B
8
C
19
-10.046
B_DA8:DT19_C
7
0.030
0.224
0.035
-0.189
-2.980
1
19
B
9
C
18
-5.376
B_DC9:DG18_C
8
-2.660
-0.176
0.379
-0.229
5.779
1
20
B
10
C
17
-13.627
B_DT10:DA17_C
9
2.411
-0.139
-0.163
-0.147
17.067
1
19
B
11
C
16
-5.551
B_DG11:DC16_C
10
18.817
-0.558
-0.033
-0.309
-1.782
1
19
B
12
C
15
-5.798
B_DG12:DC15_C
11
-1.418
-0.275
-0.111
-0.275
9.411
1
19
B
13
C
14
-4.405
B_DG13:DC14_C
12
-5.196
-0.618
0.176
-0.332
3.536
43.991
A
A
1
2
12.750
C
C
26
25
3.720
9.477
0.159
-0.521
AA_DC1DC2:DG25DG26_CC
1
2.739
-3.685
42.924
-1.701
0.078
3.319
33.236
A
A
2
3
-10.611
C
C
25
24
3.337
-5.988
0.312
-1.048
AA_DC2DA3:DT24DG25_CC
2
-7.480
13.256
31.862
-0.791
-1.847
3.663
39.233
A
A
3
4
-8.785
C
C
24
23
3.573
-5.878
-0.508
-0.849
AA_DA3DA4:DT23DT24_CC
3
-0.423
0.632
38.805
-0.484
0.701
3.197
32.522
A
A
4
5
-10.376
C
C
23
22
3.146
-5.780
-0.132
-0.615
AA_DA4DA5:DT22DT23_CC
4
1.358
-2.438
31.989
-0.110
0.467
3.146
39.262
A
A
5
6
-8.839
C
C
22
21
3.044
-5.912
-0.142
-0.915
AA_DA5DG6:DC21DT22_CC
5
-3.213
4.803
38.704
-0.689
-0.153
3.225
33.674
B
B
8
9
-1.823
C
C
19
18
3.205
-1.055
-0.180
-0.604
BB_DA8DC9:DG18DT19_CC
6
-2.883
4.984
33.538
-0.873
-0.151
3.025
33.635
B
B
9
10
-6.005
C
C
18
17
3.018
-3.457
0.076
-0.423
BB_DC9DT10:DA17DG18_CC
7
4.976
-8.644
33.100
-0.205
0.625
3.447
34.656
B
B
10
11
-16.156
C
C
17
16
3.376
-9.496
0.536
-0.938
BB_DT10DG11:DC16DA17_CC
8
-2.952
5.022
33.240
-0.019
-1.384
4.254
45.884
B
B
11
12
-15.189
C
C
16
15
4.166
-11.707
0.123
-0.905
BB_DG11DG12:DC15DC16_CC
9
4.408
-5.720
44.235
0.171
0.344
3.073
29.297
B
B
12
13
12.909
C
C
15
14
3.098
6.456
-0.413
0.098
BB_DG12DG13:DC14DC15_CC
10
-4.191
8.380
28.289
-1.145
-0.053
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_conn_type
struct_site
chem_comp_atom
chem_comp_bond
pdbx_nmr_spectrometer
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
Data collection
1
0
2001-06-06
1
1
2007-10-16
1
2
2011-07-13
1
3
2022-02-23
1
4
2023-12-27
1
5
2024-07-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_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_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_pdbx_nmr_spectrometer.model
Ensemble: 1G5D has the same sequence and contains an abasic site (alpha anomer) instead of the phosphoglycolate lesion
Minimized Average Structure: 1GIZ has the same sequence and contains an abasic site (alpha anomer) instead of the phosphoglycolate lesion
Ensemble: 1G5E has the same sequence and contains an abasic site (beta anomer) instead of the phosphoglycolate lesion
Minimized Average Structure: 1GJ0 has the same sequence and contains an abasic site (beta anomer) instead of the phosphoglycolate lesion
Ensemble: 1G5K is the structure of the oligonucleotide containing the phosphoglycolate lesion without the bleomycin bound.
Minimized Average Structure: 1GJ1 is the structure of the oligonucleotide containing the phosphoglycolate lesion without the bleomycin bound.
Ensemble: 1G5L is Co(III)-Bleomycin-OOH bound to an oligonucleotide containing a phosphoglycolate lesion
RCSB
Y
RCSB
2000-11-01
REL
PGA
2-PHOSPHOGLYCOLIC ACID
3CO
COBALT (III) ION
O
OXYGEN ATOM
BLB
BLEOMYCIN B2
PEO
HYDROGEN PEROXIDE
DNA WAS SYNTHESIZED AS A DOUBLE HAIRPIN, BUT FOR MODELING PURPOSED WAS TREATED AS TWO STRANDS OF DNA; THE HEXAETHYLENE GLYCOL SPACERS WERE NOT INCLUDED IN THE MODELING
1
NOESY
TOCSY
PE-COSY
WATERGATE-NOESY
31P- HCOSY
13C-HSQC
ROESY
40 mM sodium phosphate buffer
6.8
ambient
293
K
40 mM sodium phosphate buffer
6.8
ambient
278
K
THE STRUCTURES ARE BASED ON 729 NOE-DERIVED DISTANCE CONSTRAINTS AND 96 DIHEDRAL ANGLE RESTRAINTS.
molecular dynamics
1.25 mM drug-DNA complex; 40 mM sodium phosphate buffer
D2O
1.25 mM drug-DNA complex; 40 mM sodium phosphate buffer
90% H2O/10% D2O
MSI
processing
Felix
95.0
Brunger
structure solution
X-PLOR
3.851
MSI
data analysis
Felix
95.0
Brunger
refinement
X-PLOR
3.851
750
Home-built
home-built
600
Home-built
home-built
2PL
6
4
PGA
PGA
7
A
3CO
10
5
3CO
3CO
14
B
O
8
6
O
O
15
B
BLB
1
7
BLB
BLB
1
C
PEO
11
8
PEO
PEO
11
C
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
G
6
n
6
DG
6
A
A
8
n
1
DA
8
B
C
9
n
2
DC
9
B
T
10
n
3
DT
10
B
G
11
n
4
DG
11
B
G
12
n
5
DG
12
B
G
13
n
6
DG
13
B
C
14
n
1
DC
14
C
C
15
n
2
DC
15
C
C
16
n
3
DC
16
C
A
17
n
4
DA
17
C
G
18
n
5
DG
18
C
T
19
n
6
DT
19
C
A
20
n
7
DA
20
C
C
21
n
8
DC
21
C
T
22
n
9
DT
22
C
T
23
n
10
DT
23
C
T
24
n
11
DT
24
C
G
25
n
12
DG
25
C
G
26
n
13
DG
26
C
author_defined_assembly
3
trimeric
C
BLB
1
G
NC
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NB
BLB
1_555
84.5
C
BLB
1
G
NC
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NG
BLB
1_555
77.6
C
BLB
1
G
NB
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NG
BLB
1_555
93.5
C
BLB
1
G
NC
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NH
BLB
1_555
154.8
C
BLB
1
G
NB
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NH
BLB
1_555
86.9
C
BLB
1
G
NG
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NH
BLB
1_555
79.3
C
BLB
1
G
NC
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NJ
BLB
1_555
114.6
C
BLB
1
G
NB
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NJ
BLB
1_555
93.5
C
BLB
1
G
NG
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NJ
BLB
1_555
166.5
C
BLB
1
G
NH
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NJ
BLB
1_555
89.6
C
BLB
1
G
NC
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
PEO
11
H
O1
PEO
1_555
93.6
C
BLB
1
G
NB
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
PEO
11
H
O1
PEO
1_555
174.2
C
BLB
1
G
NG
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
PEO
11
H
O1
PEO
1_555
91.5
C
BLB
1
G
NH
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
PEO
11
H
O1
PEO
1_555
97.0
C
BLB
1
G
NJ
BLB
1_555
B
3CO
14
E
CO
3CO
1_555
C
PEO
11
H
O1
PEO
1_555
82.3
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
C
CO
HB2
3CO
BLB
14
1
1.41
1
C
C
OP1
HO2
DA
BLB
20
1
1.50
1
4.63
0.30
108.30
112.93
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.08
0.60
118.90
122.98
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
1
4.29
0.60
118.60
122.89
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
4.03
0.60
118.60
122.63
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
7.01
0.70
119.90
126.91
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
-5.02
0.70
108.00
102.98
B
B
B
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
4.15
0.60
118.60
122.75
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
1
3.07
0.30
108.30
111.37
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-2.67
0.40
121.90
119.23
B
B
B
N3
C4
C5
DC
DC
DC
9
9
9
N
1
4.32
0.70
118.00
122.32
B
B
B
N3
C4
N4
DC
DC
DC
9
9
9
N
1
3.86
0.30
108.30
112.16
B
B
B
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
-4.58
0.60
122.90
118.32
B
B
B
C6
C5
C7
DT
DT
DT
10
10
10
N
1
-3.67
0.60
123.90
120.23
B
B
B
N1
C2
N3
DG
DG
DG
11
11
11
N
1
6.00
0.70
119.90
125.90
B
B
B
N3
C2
N2
DG
DG
DG
11
11
11
N
1
5.97
0.70
119.90
125.87
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
1
5.98
0.70
119.90
125.88
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
1
3.91
0.30
108.30
112.21
C
C
C
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
12.98
1.60
120.90
133.88
C
C
C
P
O5'
C5'
DC
DC
DC
15
15
15
N
1
3.71
0.60
118.90
122.61
C
C
C
N1
C2
O2
DC
DC
DC
15
15
15
N
1
-4.69
0.70
121.90
117.21
C
C
C
N3
C2
O2
DC
DC
DC
15
15
15
N
1
2.20
0.30
108.30
110.50
C
C
C
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
3.82
0.60
118.90
122.72
C
C
C
N1
C2
O2
DC
DC
DC
16
16
16
N
1
5.98
0.60
118.60
124.58
C
C
C
N1
C6
N6
DA
DA
DA
17
17
17
N
1
-5.59
0.80
123.70
118.11
C
C
C
C5
C6
N6
DA
DA
DA
17
17
17
N
1
7.52
1.20
119.70
127.22
C
C
C
C3'
O3'
P
DA
DA
DG
17
17
18
Y
1
-2.53
0.40
106.40
103.87
C
C
C
C8
N9
C4
DG
DG
DG
18
18
18
N
1
-4.93
0.80
105.90
100.97
C
C
C
O4'
C1'
C2'
DT
DT
DT
19
19
19
N
1
4.88
0.60
119.00
123.88
C
C
C
C4
C5
C7
DT
DT
DT
19
19
19
N
1
-5.79
0.60
122.90
117.11
C
C
C
C6
C5
C7
DT
DT
DT
19
19
19
N
1
-5.21
0.80
105.90
100.69
C
C
C
O4'
C1'
C2'
DA
DA
DA
20
20
20
N
1
-5.05
0.70
108.00
102.95
C
C
C
O4'
C1'
N9
DA
DA
DA
20
20
20
N
1
9.97
1.20
119.70
129.67
C
C
C
C3'
O3'
P
DC
DC
DT
21
21
22
Y
1
10.45
0.60
119.00
129.45
C
C
C
C4
C5
C7
DT
DT
DT
22
22
22
N
1
-12.61
0.60
122.90
110.29
C
C
C
C6
C5
C7
DT
DT
DT
22
22
22
N
1
11.97
1.20
119.70
131.67
C
C
C
C3'
O3'
P
DT
DT
DT
22
22
23
Y
1
4.38
0.60
119.00
123.38
C
C
C
C4
C5
C7
DT
DT
DT
23
23
23
N
1
-7.11
0.60
122.90
115.79
C
C
C
C6
C5
C7
DT
DT
DT
23
23
23
N
1
11.35
0.60
119.00
130.35
C
C
C
C4
C5
C7
DT
DT
DT
24
24
24
N
1
-13.61
0.60
122.90
109.29
C
C
C
C6
C5
C7
DT
DT
DT
24
24
24
N
1
8.42
1.20
119.70
128.12
C
C
C
C3'
O3'
P
DT
DT
DG
24
24
25
Y
1
4.51
0.70
119.90
124.41
C
C
C
N3
C2
N2
DG
DG
DG
25
25
25
N
1
5.82
0.70
119.90
125.72
C
C
C
N3
C2
N2
DG
DG
DG
26
26
26
N
1
C
C
N9
C4
DA
DA
17
17
0.036
0.006
1.374
1.410
N
CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
7
N
N
8
N
N
covale
1.600
one
A
DG
6
A
O3'
DG
6
1_555
A
PGA
7
D
P
PGA
1_555
covale
1.481
both
B
DA
8
B
P
DA
1
1_555
B
O
15
F
O
O
1_555
metalc
2.000
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NC
BLB
1_555
metalc
1.950
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NB
BLB
1_555
metalc
1.854
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NG
BLB
1_555
metalc
1.926
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NH
BLB
1_555
metalc
1.918
B
3CO
14
E
CO
3CO
1_555
C
BLB
1
G
NJ
BLB
1_555
metalc
2.033
B
3CO
14
E
CO
3CO
1_555
C
PEO
11
H
O1
PEO
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
C
DG
26
C
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
C
DG
26
C
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
C
DG
26
C
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
C
DG
25
C
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
C
DG
25
C
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
C
DG
25
C
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
C
DT
24
C
N3
DT
11
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
C
DT
24
C
O4
DT
11
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
C
DT
23
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
C
DT
23
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
C
DT
22
C
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
C
DT
22
C
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
C
DC
21
C
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
C
DC
21
C
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
C
DC
21
C
N4
DC
8
1_555
hydrog
WATSON-CRICK
B
DA
8
B
N1
DA
1
1_555
C
DT
19
C
N3
DT
6
1_555
hydrog
WATSON-CRICK
B
DA
8
B
N6
DA
1
1_555
C
DT
19
C
O4
DT
6
1_555
hydrog
WATSON-CRICK
B
DC
9
B
N3
DC
2
1_555
C
DG
18
C
N1
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
9
B
N4
DC
2
1_555
C
DG
18
C
O6
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
9
B
O2
DC
2
1_555
C
DG
18
C
N2
DG
5
1_555
hydrog
WATSON-CRICK
B
DT
10
B
N3
DT
3
1_555
C
DA
17
C
N1
DA
4
1_555
hydrog
WATSON-CRICK
B
DT
10
B
O4
DT
3
1_555
C
DA
17
C
N6
DA
4
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N1
DG
4
1_555
C
DC
16
C
N3
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
N2
DG
4
1_555
C
DC
16
C
O2
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
11
B
O6
DG
4
1_555
C
DC
16
C
N4
DC
3
1_555
hydrog
WATSON-CRICK
B
DG
12
B
N1
DG
5
1_555
C
DC
15
C
N3
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
12
B
N2
DG
5
1_555
C
DC
15
C
O2
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
12
B
O6
DG
5
1_555
C
DC
15
C
N4
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
13
B
N1
DG
6
1_555
C
DC
14
C
N3
DC
1
1_555
hydrog
WATSON-CRICK
B
DG
13
B
N2
DG
6
1_555
C
DC
14
C
O2
DC
1
1_555
hydrog
WATSON-CRICK
B
DG
13
B
O6
DG
6
1_555
C
DC
14
C
N4
DC
1
1_555
DNA
DAMAGED DNA, DNA-DRUG COMPLEX, INTERCALATION, DNA
1GJ2
PDB
1
1GJ2
1GJ2
PDB
2
1GJ2
1GJ2
PDB
3
1GJ2
1
6
1GJ2
1
6
1GJ2
A
1
1
6
8
13
1GJ2
8
13
1GJ2
B
2
1
6
14
26
1GJ2
14
26
1GJ2
C
3
1
13
BINDING SITE FOR RESIDUE PGA A 7
A
PGA
7
Software
2
BINDING SITE FOR RESIDUE 3CO B 14
B
3CO
14
Software
2
BINDING SITE FOR RESIDUE O B 15
B
O
15
Software
1
BINDING SITE FOR RESIDUE BLB C 1
C
BLB
1
Software
13
BINDING SITE FOR RESIDUE PEO C 11
C
PEO
11
Software
3
A
DG
6
A
DG
6
2
1_555
C
BLB
1
G
BLB
2
1_555
C
BLB
1
G
BLB
2
1_555
C
PEO
11
H
PEO
2
1_555
B
DA
8
B
DA
1
1
1_555
A
DG
6
A
DG
6
13
1_555
A
PGA
7
D
PGA
13
1_555
B
DA
8
B
DA
1
13
1_555
B
DC
9
B
DC
2
13
1_555
B
DT
10
B
DT
3
13
1_555
B
DG
11
B
DG
4
13
1_555
B
DG
12
B
DG
5
13
1_555
B
DG
13
B
DG
6
13
1_555
B
3CO
14
E
3CO
13
1_555
C
PEO
11
H
PEO
13
1_555
C
DG
18
C
DG
5
13
1_555
C
DT
19
C
DT
6
13
1_555
C
DA
20
C
DA
7
13
1_555
B
3CO
14
E
3CO
3
1_555
C
BLB
1
G
BLB
3
1_555
C
DT
19
C
DT
6
3
1_555
1
P 1