1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sastry, M.
Fiala, R.
Lipman, R.
Tomasz, M.
Patel, D.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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 H13 N4 O7 P
332.207
y
2'-DEOXYINOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C14 H16 N4 O4
304.301
CARBAMIC ACID 2,6-DIAMINO-5-METHYL-4,7-DIOXO-2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8-YLMETHYL ESTER
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
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
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
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
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
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
Y
120
N
N
Y
121
N
C
Y
122
N
N
Y
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
N
Y
129
N
C
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
O
N
144
N
P
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
C
N
149
R
C
N
150
N
O
N
151
S
C
N
152
N
O
N
153
N
C
N
154
R
C
N
155
N
N
N
156
N
C
N
157
N
O
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
C
N
162
N
C
N
163
N
C
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
C
N
180
R
C
N
181
N
N
N
182
N
C
Y
183
N
N
Y
184
N
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
N
N
191
N
C
N
192
N
O
Y
193
N
C
Y
194
N
C
Y
195
N
C
N
196
N
C
N
197
N
O
N
198
N
C
N
199
N
O
N
200
N
N
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
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
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
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
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
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
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
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
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
Y
136
N
sing
Y
137
N
sing
Y
138
N
doub
N
139
N
sing
Y
140
N
sing
N
141
N
sing
Y
142
N
doub
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
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
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
doub
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
N
196
N
sing
N
197
N
sing
N
198
N
sing
Y
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
doub
N
207
N
sing
N
208
N
sing
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
Y
216
N
sing
Y
217
N
doub
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
doub
N
224
N
sing
N
225
N
sing
N
226
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
247
338
359
10.1006/jmbi.1994.0143
7707379
Solution structure of the monoalkylated mitomycin C-DNA complex.
1995
10.2210/pdb199d/pdb
pdb_0000199d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2701.770
DNA (5'-D(*(DI)P*CP*AP*CP*GP*TP*CP*(DI)P*T)-3')
1
syn
polymer
2740.812
DNA (5'-D(*AP*CP*GP*AP*CP*GP*TP*GP*C)-3')
1
syn
polymer
CHEMICALLY SYNTHESIZED
304.301
CARBAMIC ACID 2,6-DIAMINO-5-METHYL-4,7-DIOXO-2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8-YLMETHYL ESTER
1
syn
non-polymer
DEOXYRIBONUCLEIC ACID
DEOXYRIBONUCLEIC ACID
no
no
(DI)(DC)(DA)(DC)(DG)(DT)(DC)(DI)(DT)
ICACGTCIT
A
polydeoxyribonucleotide
no
no
(DA)(DC)(DG)(DA)(DC)(DG)(DT)(DG)(DC)
ACGACGTGC
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-11.752
1
19
A
2
B
17
-2.730
A_DC2:DG17_B
1
-10.574
0.374
0.423
-0.335
-6.800
1
20
A
3
B
16
-4.971
A_DA3:DT16_B
2
-28.159
0.066
-0.300
-0.247
-4.036
1
19
A
4
B
15
-5.442
A_DC4:DG15_B
3
-14.332
0.777
0.143
-0.426
-9.539
1
19
A
5
B
14
-1.377
A_DG5:DC14_B
4
-2.490
-0.579
-0.167
-0.261
15.817
1
20
A
6
B
13
-1.575
A_DT6:DA13_B
5
-5.212
0.092
-0.125
-0.233
-2.978
1
19
A
7
B
12
0.492
A_DC7:DG12_B
6
-7.771
0.338
0.189
-0.238
9.396
1
20
A
9
B
10
-6.103
A_DT9:DA10_B
7
-4.428
-0.292
-0.043
-0.131
1.758
34.767
A
A
2
3
32.512
B
B
17
16
2.899
18.478
-0.288
-1.364
AA_DC2DA3:DT16DG17_BB
1
1.055
-1.857
29.561
-4.466
0.606
3.034
33.264
A
A
3
4
-1.488
B
B
16
15
3.006
-0.849
-0.255
-1.017
AA_DA3DC4:DG15DT16_BB
2
-5.212
9.141
32.854
-1.645
-0.363
2.086
27.321
A
A
4
5
24.379
B
B
15
14
2.977
11.184
-0.213
-1.548
AA_DC4DG5:DC14DG15_BB
3
1.393
-3.036
24.929
-5.533
0.733
2.454
34.212
A
A
5
6
2.619
B
B
14
13
2.450
1.540
-0.075
0.141
AA_DG5DT6:DA13DC14_BB
4
0.001
-0.001
34.178
0.057
0.127
3.090
43.342
A
A
6
7
16.329
B
B
13
12
3.484
11.910
-0.007
-1.006
AA_DT6DC7:DG12DA13_BB
5
-2.914
3.995
41.652
-2.553
-0.282
5.201
62.137
A
A
7
9
12.516
B
B
12
10
5.804
12.815
-0.397
-2.245
AA_DC7DT9:DA10DG12_BB
6
7.712
-7.532
60.486
-3.182
0.991
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
entity
pdbx_entity_src_syn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Data collection
Source and taxonomy
Structure summary
1
0
1995-02-07
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-03-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_entity.details
Y
BNL
1994-12-01
REL
MOC
CARBAMIC ACID 2,6-DIAMINO-5-METHYL-4,7-DIOXO-2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8-YLMETHYL ESTER
CHEMICALLY SYNTHESIZED
sample
CHEMICALLY SYNTHESIZED
sample
all calculated structures submitted
3
3
THREE STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITOMYCIN C ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES DERIVED FROM NMR DATA. THE THREE DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL THREE STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 90, 120, 200 AND 300 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE THREE FINAL STRUCTURES ARE: MDL1 MDL2 MDL3 R(1/6) FACTOR 0.027 0.026 0.026 BOND (ANG) 0.008 0.008 0.008 ANGLE (DEG) 2.913 2.931 2.949 IMPROPER (DEG) 0.361 0.393 0.372
MOLECULAR DYNAMICS, MATRIX RELAXATION
BRUNGER
refinement
X-PLOR
MOC
19
3
MOC
MOC
19
A
DI
1
n
1
DI
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
C
4
n
4
DC
4
A
G
5
n
5
DG
5
A
T
6
n
6
DT
6
A
C
7
n
7
DC
7
A
DI
8
n
8
DI
8
A
T
9
n
9
DT
9
A
A
10
n
1
DA
10
B
C
11
n
2
DC
11
B
G
12
n
3
DG
12
B
A
13
n
4
DA
13
B
C
14
n
5
DC
14
B
G
15
n
6
DG
15
B
T
16
n
7
DT
16
B
G
17
n
8
DG
17
B
C
18
n
9
DC
18
B
author_defined_assembly
2
dimeric
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
3.62
0.60
106.00
109.62
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
1
-4.95
0.80
105.90
100.95
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
1
10.39
1.20
119.70
130.09
A
A
A
C3'
O3'
P
DC
DC
DA
2
2
3
Y
1
-5.24
0.70
108.00
102.76
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
9.12
1.20
119.70
128.82
A
A
A
C3'
O3'
P
DA
DA
DC
3
3
4
Y
1
-4.49
0.70
102.20
97.71
A
A
A
C4'
C3'
C2'
DC
DC
DC
4
4
4
N
1
-5.62
0.80
105.90
100.28
A
A
A
O4'
C1'
C2'
DC
DC
DC
4
4
4
N
1
3.79
0.60
118.90
122.69
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
1
-5.35
0.80
105.90
100.55
A
A
A
O4'
C1'
C2'
DG
DG
DG
5
5
5
N
1
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
5.47
0.30
108.30
113.77
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
-9.13
1.00
110.10
100.97
B
B
B
C1'
O4'
C4'
DA
DA
DA
10
10
10
N
1
-6.05
0.80
105.90
99.85
B
B
B
O4'
C1'
C2'
DA
DA
DA
10
10
10
N
1
6.13
0.30
108.30
114.43
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
6.74
1.10
109.80
116.54
B
B
B
C5'
C4'
O4'
DG
DG
DG
12
12
12
N
1
-5.62
0.80
105.90
100.28
B
B
B
O4'
C1'
C2'
DG
DG
DG
12
12
12
N
1
6.46
0.30
108.30
114.76
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-4.28
0.70
108.00
103.72
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
3.66
0.60
118.90
122.56
B
B
B
N1
C2
O2
DC
DC
DC
14
14
14
N
1
7.11
1.10
109.80
116.91
B
B
B
C5'
C4'
O4'
DG
DG
DG
15
15
15
N
1
-6.87
0.80
105.90
99.03
B
B
B
O4'
C1'
C2'
DG
DG
DG
15
15
15
N
1
2.50
0.30
108.30
110.80
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
-4.80
0.80
105.90
101.10
B
B
B
O4'
C1'
C2'
DT
DT
DT
16
16
16
N
1
8.68
0.30
108.30
116.98
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
5.65
0.30
108.30
113.95
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
-5.11
0.70
102.20
97.09
B
B
B
C4'
C3'
C2'
DC
DC
DC
18
18
18
N
1
5.46
0.30
108.30
113.76
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
2
3.70
0.60
106.00
109.70
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
2
-5.30
0.80
105.90
100.60
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
2
-7.90
0.80
105.90
98.00
A
A
A
O4'
C1'
C2'
DC
DC
DC
4
4
4
N
2
4.53
0.30
108.30
112.83
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
3.67
0.60
118.90
122.57
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
2
-4.26
0.70
102.20
97.94
A
A
A
C4'
C3'
C2'
DG
DG
DG
5
5
5
N
2
-5.17
0.80
105.90
100.73
A
A
A
O4'
C1'
C2'
DG
DG
DG
5
5
5
N
2
5.04
0.30
108.30
113.34
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
3.68
0.30
108.30
111.98
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
-9.33
1.00
110.10
100.77
B
B
B
C1'
O4'
C4'
DA
DA
DA
10
10
10
N
2
-4.94
0.80
105.90
100.96
B
B
B
O4'
C1'
C2'
DA
DA
DA
10
10
10
N
2
6.39
0.30
108.30
114.69
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
2
8.77
1.20
119.70
128.47
B
B
B
C3'
O3'
P
DA
DA
DC
10
10
11
Y
2
8.27
1.10
109.80
118.07
B
B
B
C5'
C4'
O4'
DG
DG
DG
12
12
12
N
2
-5.44
0.80
105.90
100.46
B
B
B
O4'
C1'
C2'
DG
DG
DG
12
12
12
N
2
10.54
1.20
119.70
130.24
B
B
B
C3'
O3'
P
DG
DG
DA
12
12
13
Y
2
-6.19
0.80
105.90
99.71
B
B
B
O4'
C1'
C2'
DG
DG
DG
15
15
15
N
2
2.10
0.30
108.30
110.40
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
2
12.12
0.30
108.30
120.42
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
2
4.59
0.30
108.30
112.89
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
2
2.13
0.30
108.30
110.43
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
3
7.21
1.20
119.70
126.91
A
A
A
C3'
O3'
P
DI
DI
DC
1
1
2
Y
3
-6.09
0.80
105.90
99.81
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
3
4.04
0.60
118.90
122.94
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
3
-4.59
0.70
108.00
103.41
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
3
-8.09
0.80
105.90
97.81
A
A
A
O4'
C1'
C2'
DC
DC
DC
4
4
4
N
3
4.92
0.30
108.30
113.22
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
3
3.73
0.60
118.90
122.63
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
3
2.50
0.30
108.30
110.80
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
3
-6.32
0.80
105.90
99.58
A
A
A
O4'
C1'
C2'
DT
DT
DT
6
6
6
N
3
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
-6.35
1.00
110.10
103.75
A
A
A
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
3
-9.19
1.00
110.10
100.91
B
B
B
C1'
O4'
C4'
DA
DA
DA
10
10
10
N
3
-5.89
0.80
105.90
100.01
B
B
B
O4'
C1'
C2'
DA
DA
DA
10
10
10
N
3
5.51
0.30
108.30
113.81
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
3
7.41
1.20
119.70
127.11
B
B
B
C3'
O3'
P
DA
DA
DC
10
10
11
Y
3
-5.01
0.80
105.90
100.89
B
B
B
O4'
C1'
C2'
DG
DG
DG
12
12
12
N
3
7.92
0.30
108.30
116.22
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
3
3.65
0.60
118.90
122.55
B
B
B
N1
C2
O2
DC
DC
DC
14
14
14
N
3
7.54
1.20
119.70
127.24
B
B
B
C3'
O3'
P
DC
DC
DG
14
14
15
Y
3
-5.78
0.80
105.90
100.12
B
B
B
O4'
C1'
C2'
DG
DG
DG
15
15
15
N
3
2.01
0.30
108.30
110.31
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
3
11.66
0.30
108.30
119.96
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
3
4.94
0.30
108.30
113.24
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
3
4.22
0.30
108.30
112.52
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
1
A
A
C5
C7
DT
DT
6
6
0.040
0.006
1.496
1.536
N
1
A
A
C5
C7
DT
DT
9
9
0.038
0.006
1.496
1.534
N
2
A
A
C5
C7
DT
DT
6
6
0.042
0.006
1.496
1.538
N
2
A
A
C5
C7
DT
DT
9
9
0.039
0.006
1.496
1.535
N
3
A
A
C5
C7
DT
DT
6
6
0.044
0.006
1.496
1.540
N
3
A
A
C5
C7
DT
DT
9
9
0.042
0.006
1.496
1.538
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
Solution structure of the monoalkylated mitomycin c-DNA complex
1
N
N
2
N
N
3
N
N
covale
1.431
none
A
DG
5
A
N2
DG
5
1_555
A
MOC
19
C
C1
MOC
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
17
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
17
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
17
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
16
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
16
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
15
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
15
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
15
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
14
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
14
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
14
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
13
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
13
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
12
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
12
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
12
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
10
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
10
B
N6
DA
1
1_555
DNA
DNA, MITOMYCIN, DOUBLE HELIX
199D
PDB
1
199D
199D
PDB
2
199D
1
9
199D
1
9
199D
A
1
1
9
10
18
199D
10
18
199D
B
2
1
9
BINDING SITE FOR RESIDUE MOC A 19
A
MOC
19
Software
6
A
DG
5
A
DG
5
6
1_555
A
DT
6
A
DT
6
6
1_555
A
DC
7
A
DC
7
6
1_555
B
DC
14
B
DC
5
6
1_555
B
DG
15
B
DG
6
6
1_555
B
DT
16
B
DT
7
6
1_555
1
P 1