0.035787
0.000000
0.000000
0.000000
0.035787
0.000000
0.000000
0.000000
0.019141
0.00000
0.00000
0.00000
Wang, A.H.-J.
Gao, Y.-G.
Liaw, Y.-C.
Li, Y.-K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
27.943
27.943
52.243
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
C27 H29 N O10
527.520
DAUNOMYCIN
DAUNORUBICIN
non-polymer
C11 H16 N5 O7 P
361.248
n
N2-METHYL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
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
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
N
22
N
H
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
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
N
Y
57
N
C
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
H
Y
72
N
C
Y
73
N
C
Y
74
N
C
Y
75
N
C
N
76
N
O
Y
77
N
C
N
78
N
C
N
79
N
O
Y
80
N
C
Y
81
N
C
N
82
N
O
Y
83
N
C
N
84
S
C
N
85
N
O
N
86
N
C
N
87
S
C
N
88
N
O
N
89
N
C
N
90
N
O
N
91
N
C
N
92
N
C
Y
93
N
C
Y
94
N
C
N
95
N
O
Y
96
N
C
N
97
N
C
N
98
N
O
Y
99
N
C
N
100
N
C
N
101
R
C
N
102
N
C
N
103
S
C
N
104
N
N
N
105
S
C
N
106
N
O
N
107
S
C
N
108
N
O
N
109
N
C
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
P
N
140
N
O
N
141
N
O
N
142
N
O
N
143
N
O
N
144
N
C
N
145
R
C
N
146
N
O
N
147
S
C
N
148
N
O
N
149
N
C
N
150
R
C
Y
151
N
N
Y
152
N
C
Y
153
N
N
Y
154
N
C
N
155
N
C
N
156
N
O
N
157
N
N
N
158
N
C
N
159
N
N
N
160
N
C
N
161
N
N
Y
162
N
C
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
O
N
180
N
H
N
181
N
H
N
182
N
MG
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
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
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
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
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
Y
75
N
doub
Y
76
N
sing
N
77
N
sing
Y
78
N
sing
N
79
N
sing
Y
80
N
doub
N
81
N
sing
N
82
N
sing
Y
83
N
sing
N
84
N
sing
N
85
N
sing
Y
86
N
doub
N
87
N
doub
N
88
N
sing
Y
89
N
doub
Y
90
N
sing
N
91
N
sing
Y
92
N
sing
N
93
N
sing
N
94
N
sing
Y
95
N
doub
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
sing
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
sing
N
113
N
sing
N
114
N
sing
Y
115
N
sing
N
116
N
sing
Y
117
N
doub
N
118
N
sing
N
119
N
sing
N
120
N
doub
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
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
doub
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
Y
169
N
sing
Y
170
N
sing
Y
171
N
doub
N
172
N
sing
Y
173
N
sing
N
174
N
sing
Y
175
N
doub
N
176
N
doub
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
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
US
Biochemistry
BICHAW
0033
0006-2960
30
3812
3815
10.1021/bi00230a002
2018756
Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC and X-ray diffraction studies.
1991
10.2210/pdb1d33/pdb
pdb_00001d33
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.00
1
DIFFRACTOMETER
RIGAKU AFC-5R
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
1824.232
5'-D(*CP*GP*CP*(G49)P*CP*G)-3'
1
syn
polymer
527.520
DAUNOMYCIN
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
65
nat
water
no
yes
(DC)(DG)(DC)(G49)(DC)(DG)
CGCGCG
A
polydeoxyribonucleotide
n
n
n
n
n
n
2.80
55.99
VAPOR DIFFUSION
6.00
pH 6.00, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
HCHO
1
BACL2
1
NA CACODYLATE
1
SPERMINE
1
WATER
2
HCHO
2
MPD
2
6.442
1
19
A
1
A
6
-2.380
A_DC1:DG6_A
1
1.246
0.228
-0.023
-0.166
-15.149
1
19
A
2
A
5
0.770
A_DG2:DC5_A
2
0.972
-0.082
-0.365
-0.187
-3.218
1
19
A
3
A
4
2.077
A_DC3:G494_A
3
-7.137
0.262
0.109
-0.254
3.218
1
19
A
4
A
3
2.077
A_G494:DC3_A
4
-7.137
-0.262
0.109
-0.254
15.149
1
19
A
5
A
2
0.770
A_DC5:DG2_A
5
0.972
0.082
-0.365
-0.187
-6.442
1
19
A
6
A
1
-2.380
A_DG6:DC1_A
6
1.246
-0.228
-0.023
-0.166
6.937
34.269
A
A
1
2
-4.210
A
A
6
5
6.982
-2.478
1.234
1.127
AA_DC1DG2:DC5DG6_AA
1
1.725
-2.931
34.140
2.742
-1.516
3.140
30.742
A
A
2
3
-6.549
A
A
5
4
3.040
-3.456
-1.169
0.026
AA_DG2DC3:G494DC5_AA
2
-3.898
7.387
30.308
0.693
1.479
3.116
36.970
A
A
3
4
12.274
A
A
4
3
3.189
7.730
0.000
-0.037
AA_DC3G494:DC3G494_AA
3
0.000
0.000
36.180
-1.073
0.000
3.140
30.742
A
A
4
5
-6.549
A
A
3
2
3.040
-3.456
1.169
0.026
AA_G494DC5:DG2DC3_AA
4
3.898
-7.387
30.308
0.693
-1.479
6.937
34.269
A
A
5
6
-4.210
A
A
2
1
6.982
-2.478
-1.234
1.127
AA_DC5DG6:DC1DG2_AA
5
-1.725
2.931
34.140
2.742
1.516
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1992-04-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_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_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1991-02-27
REL
DM1
DAUNOMYCIN
MG
MAGNESIUM ION
HOH
water
A METHYLENE GROUP LINKS THE N3* ATOM OF DAUNOMYCIN
AND N2 G A 4.
DM1
4
2
DM1
DM1
7
A
MG
8
3
MG
MG
8
A
HOH
9
4
HOH
HOH
9
A
HOH
10
4
HOH
HOH
10
A
HOH
11
4
HOH
HOH
11
A
HOH
12
4
HOH
HOH
12
A
HOH
13
4
HOH
HOH
13
A
HOH
14
4
HOH
HOH
14
A
HOH
15
4
HOH
HOH
15
A
HOH
16
4
HOH
HOH
16
A
HOH
17
4
HOH
HOH
17
A
HOH
18
4
HOH
HOH
18
A
HOH
19
4
HOH
HOH
19
A
HOH
20
4
HOH
HOH
20
A
HOH
21
4
HOH
HOH
21
A
HOH
22
4
HOH
HOH
22
A
HOH
23
4
HOH
HOH
23
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
26
4
HOH
HOH
26
A
HOH
27
4
HOH
HOH
27
A
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
31
4
HOH
HOH
31
A
HOH
32
4
HOH
HOH
32
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
35
4
HOH
HOH
35
A
HOH
36
4
HOH
HOH
36
A
HOH
37
4
HOH
HOH
37
A
HOH
38
4
HOH
HOH
38
A
HOH
39
4
HOH
HOH
39
A
HOH
40
4
HOH
HOH
40
A
HOH
41
4
HOH
HOH
41
A
HOH
42
4
HOH
HOH
42
A
HOH
43
4
HOH
HOH
43
A
HOH
44
4
HOH
HOH
44
A
HOH
45
4
HOH
HOH
45
A
HOH
46
4
HOH
HOH
46
A
HOH
47
4
HOH
HOH
47
A
HOH
48
4
HOH
HOH
48
A
HOH
49
4
HOH
HOH
49
A
HOH
50
4
HOH
HOH
50
A
HOH
51
4
HOH
HOH
51
A
HOH
52
4
HOH
HOH
52
A
HOH
53
4
HOH
HOH
53
A
HOH
54
4
HOH
HOH
54
A
HOH
55
4
HOH
HOH
55
A
HOH
56
4
HOH
HOH
56
A
HOH
57
4
HOH
HOH
57
A
HOH
58
4
HOH
HOH
58
A
HOH
59
4
HOH
HOH
59
A
HOH
60
4
HOH
HOH
60
A
HOH
61
4
HOH
HOH
61
A
HOH
62
4
HOH
HOH
62
A
HOH
63
4
HOH
HOH
63
A
HOH
64
4
HOH
HOH
64
A
HOH
65
4
HOH
HOH
65
A
HOH
66
4
HOH
HOH
66
A
HOH
67
4
HOH
HOH
67
A
HOH
68
4
HOH
HOH
68
A
HOH
69
4
HOH
HOH
69
A
HOH
70
4
HOH
HOH
70
A
HOH
71
4
HOH
HOH
71
A
HOH
72
4
HOH
HOH
72
A
HOH
73
4
HOH
HOH
73
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
+G
4
n
4
G49
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
author_and_software_defined_assembly
PISA
2
dimeric
4290
-1.1
1690
A
G49
4
A
G49
4
DG
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_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
27.9430000000
27.9430000000
26.1215000000
1
A
A
O
O
HOH
HOH
71
73
1.45
1
A
A
O
O
HOH
HOH
71
72
1.46
1
A
A
O
O
HOH
HOH
23
67
1.96
1
11.29
1.20
119.70
130.99
A
A
A
C3'
O3'
P
DC
DC
DG
1
1
2
Y
1
-5.68
0.80
102.40
96.72
A
A
A
C3'
C2'
C1'
DG
DG
DG
2
2
2
N
1
6.52
0.30
108.30
114.82
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
12.30
1.20
119.70
132.00
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
3.59
0.50
119.90
123.49
A
A
A
C2
N3
C4
DC
DC
DC
3
3
3
N
1
-3.17
0.40
121.90
118.73
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
-5.71
0.80
102.40
96.69
A
A
A
C3'
C2'
C1'
DC
DC
DC
5
5
5
N
1
9.88
0.30
108.30
118.18
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
7.65
1.10
110.50
118.15
A
A
A
O3'
P
OP1
DC
DG
DG
5
6
6
Y
1
-3.66
0.60
125.10
121.44
A
A
A
C6
N1
C2
DG
DG
DG
6
6
6
N
1
4.62
0.50
111.50
116.12
A
A
A
C5
C6
N1
DG
DG
DG
6
6
6
N
1
-4.16
0.60
128.60
124.44
A
A
A
C5
C6
O6
DG
DG
DG
6
6
6
N
1
A
A
P
O5'
DC
DC
5
5
0.091
0.010
1.593
1.684
N
1
A
A
N3
C4
DC
DC
5
5
0.044
0.007
1.335
1.379
N
1
A
A
O
O
HOH
HOH
42
56
2.01
1_555
4_454
0.185
1.500
2229
1
3.000
TR
isotropic
TR
isotropic
1.500
65
225
40
120
0
0.016
fix
fix
1.500
1D33
3.000
1
refinement
NUCLSQ
Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC and X-RAY diffraction studies
1
N
N
2
N
N
3
N
N
4
N
N
covale
1.611
both
A
DC
3
A
O3'
DC
3
1_555
A
G49
4
A
P
G49
4
1_555
covale
1.633
one
A
G49
4
A
O3'
G49
4
1_555
A
DC
5
A
P
DC
5
1_555
covale
1.532
none
A
G49
4
A
CM2
G49
4
1_555
A
DM1
7
B
N3'
DM1
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
6
A
N1
DG
6
8_665
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
6
A
O6
DG
6
8_665
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
6
A
N2
DG
6
8_665
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
5
A
N3
DC
5
8_665
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
5
A
O2
DC
5
8_665
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
5
A
N4
DC
5
8_665
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
A
G49
4
A
N1
G49
4
8_665
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
A
G49
4
A
O6
G49
4
8_665
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
A
G49
4
A
N2
G49
4
8_665
hydrog
WATSON-CRICK
A
G49
4
A
N1
G49
4
1_555
A
DC
3
A
N3
DC
3
8_665
hydrog
WATSON-CRICK
A
G49
4
A
N2
G49
4
1_555
A
DC
3
A
O2
DC
3
8_665
hydrog
WATSON-CRICK
A
G49
4
A
O6
G49
4
1_555
A
DC
3
A
N4
DC
3
8_665
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
2
A
N1
DG
2
8_665
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
2
A
O6
DG
2
8_665
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
2
A
N2
DG
2
8_665
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
1
A
N3
DC
1
8_665
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
1
A
O2
DC
1
8_665
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
1
A
N4
DC
1
8_665
DNA
RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA
1D33
PDB
1
1D33
1
6
1D33
1
6
1D33
A
1
1
6
BINDING SITE FOR RESIDUE DM1 A 7
A
DM1
7
Software
12
BINDING SITE FOR RESIDUE MG A 8
A
MG
8
Software
5
A
DC
1
A
DC
1
12
8_665
A
DG
2
A
DG
2
12
8_665
A
DC
3
A
DC
3
12
8_665
A
G49
4
A
G49
4
12
1_555
A
DC
5
A
DC
5
12
1_555
A
DG
6
A
DG
6
12
1_555
A
MG
8
C
MG
12
1_555
A
HOH
29
D
HOH
12
1_555
A
HOH
34
D
HOH
12
1_555
A
HOH
36
D
HOH
12
1_555
A
HOH
60
D
HOH
12
1_555
A
HOH
71
D
HOH
12
1_555
A
DG
6
A
DG
6
5
1_555
A
DM1
7
B
DM1
5
1_555
A
HOH
9
D
HOH
5
1_555
A
HOH
10
D
HOH
5
1_555
A
HOH
11
D
HOH
5
1_555
92
tetragonal
P 41 21 2