0.035804
0.000000
0.000000
0.000000
0.035804
0.000000
0.000000
0.000000
0.017340
0.00000
0.00000
0.00000
Chen, X.
Ramakrishnan, B.
Rao, S.T.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
27.930
27.930
57.670
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H13 N4 O7 P
332.207
y
2'-DEOXYINOSINE-5'-MONOPHOSPHATE
DNA linking
C22 H27 N9 O4
481.508
DISTAMYCIN A
DISTAMYCIN; STALLIMYCIN
non-polymer
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
Y
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
C
N
71
N
O
N
72
N
N
Y
73
N
C
Y
74
N
C
Y
75
N
C
Y
76
N
N
Y
77
N
C
N
78
N
C
N
79
N
C
N
80
N
O
N
81
N
N
Y
82
N
C
Y
83
N
C
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
Y
91
N
C
Y
92
N
C
Y
93
N
C
Y
94
N
N
Y
95
N
C
N
96
N
C
N
97
N
C
N
98
N
O
N
99
N
N
N
100
N
C
N
101
N
C
N
102
N
C
N
103
N
N
N
104
N
N
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
O
N
133
N
H
N
134
N
H
N
135
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
doub
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
Y
78
N
sing
Y
79
N
doub
Y
80
N
doub
N
81
N
sing
Y
82
N
sing
N
83
N
sing
Y
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
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
Y
94
N
sing
Y
95
N
doub
Y
96
N
doub
N
97
N
sing
Y
98
N
sing
N
99
N
sing
Y
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
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
Y
110
N
sing
Y
111
N
doub
Y
112
N
doub
N
113
N
sing
Y
114
N
sing
N
115
N
sing
Y
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
doub
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
doub
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
1
169
175
10.1038/nsb0394-169
7656035
Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.
1994
10.2210/pdb159d/pdb
pdb_0000159d
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
AREA DETECTOR
SIEMENS
x-ray
1
1.0
ROTATING ANODE
2368.537
DNA (5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3')
1
syn
polymer
481.508
DISTAMYCIN A
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
65
nat
water
no
no
(DI)(DC)(DI)(DC)(DI)(DC)(DI)(DC)
ICICICIC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
2.37
48.19
VAPOR DIFFUSION, HANGING DROP
7.00
pH 7.00, VAPOR DIFFUSION, HANGING DROP
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
WATER
2
MPD
2
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1995-02-07
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1994-02-10
REL
REL
DMY
DISTAMYCIN A
MG
MAGNESIUM ION
HOH
water
DMY
9
2
DMY
DMY
9
A
MG
10
3
MG
MG
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
HOH
74
4
HOH
HOH
74
A
HOH
75
4
HOH
HOH
75
A
I
1
n
1
DI
1
A
C
2
n
2
DC
2
A
I
3
n
3
DI
3
A
C
4
n
4
DC
4
A
I
5
n
5
DI
5
A
C
6
n
6
DC
6
A
I
7
n
7
DI
7
A
C
8
n
8
DC
8
A
author_defined_assembly
2
dimeric
A
DC
6
A
OP2
DC
6
1_555
A
MG
10
C
MG
MG
1_555
A
HOH
11
D
O
HOH
1_555
89.4
A
DC
6
A
OP2
DC
6
1_555
A
MG
10
C
MG
MG
1_555
A
HOH
19
D
O
HOH
1_555
87.1
A
HOH
11
D
O
HOH
1_555
A
MG
10
C
MG
MG
1_555
A
HOH
19
D
O
HOH
1_555
91.9
A
DC
6
A
OP2
DC
6
1_555
A
MG
10
C
MG
MG
1_555
A
HOH
20
D
O
HOH
1_555
98.4
A
HOH
11
D
O
HOH
1_555
A
MG
10
C
MG
MG
1_555
A
HOH
20
D
O
HOH
1_555
171.6
A
HOH
19
D
O
HOH
1_555
A
MG
10
C
MG
MG
1_555
A
HOH
20
D
O
HOH
1_555
91.5
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_555
x,-y,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
28.8350000000
1
A
DI
3
0.074
SIDE CHAIN
1
A
DI
5
0.089
SIDE CHAIN
1
A
DC
6
0.056
SIDE CHAIN
1
3.24
0.30
108.30
111.54
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
7.87
1.10
110.50
118.37
A
A
A
O3'
P
OP1
DC
DI
DI
2
3
3
Y
1
-5.09
0.80
105.90
100.81
A
A
A
O4'
C1'
C2'
DC
DC
DC
4
4
4
N
1
3.65
0.60
118.90
122.55
A
A
A
N1
C2
O2
DC
DC
DC
4
4
4
N
1
4.07
0.60
118.90
122.97
A
A
A
N1
C2
O2
DC
DC
DC
6
6
6
N
1
7.55
1.10
110.50
118.05
A
A
A
O3'
P
OP2
DC
DI
DI
6
7
7
Y
1
9.22
1.10
110.50
119.72
A
A
A
O3'
P
OP2
DI
DC
DC
7
8
8
Y
1
A
A
O
O
HOH
HOH
41
41
1.83
1_555
8_555
0.1500000
0.1500000
1.800
10.000
2254
1
2.000
TR
isotropic
TR
isotropic
1.800
10.000
65
258
36
157
0
0.011
3.50
38.4
15.30
fix
fix
1.800
16.000
159D
10245
2423
1
refinement
X-PLOR
SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX
1
N
N
2
N
N
3
N
N
4
N
N
metalc
1.933
A
DC
6
A
OP2
DC
6
1_555
A
MG
10
C
MG
MG
1_555
metalc
2.049
A
MG
10
C
MG
MG
1_555
A
HOH
11
D
O
HOH
1_555
metalc
2.018
A
MG
10
C
MG
MG
1_555
A
HOH
19
D
O
HOH
1_555
metalc
2.085
A
MG
10
C
MG
MG
1_555
A
HOH
20
D
O
HOH
1_555
DNA
B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA
159D
PDB
1
159D
1
8
159D
1
8
159D
A
1
1
8
BINDING SITE FOR RESIDUE DMY A 9
A
DMY
9
Software
16
BINDING SITE FOR RESIDUE MG A 10
A
MG
10
Software
6
A
DC
2
A
DC
2
16
1_555
A
DI
3
A
DI
3
16
1_555
A
DI
3
A
DI
3
16
6_555
A
DC
4
A
DC
4
16
6_555
A
DI
5
A
DI
5
16
6_555
A
DC
6
A
DC
6
16
6_555
A
DC
6
A
DC
6
16
8_565
A
DI
7
A
DI
7
16
6_555
A
DC
8
A
DC
8
16
6_555
A
HOH
14
D
HOH
16
1_555
A
HOH
22
D
HOH
16
6_555
A
HOH
33
D
HOH
16
6_555
A
HOH
33
D
HOH
16
1_555
A
HOH
49
D
HOH
16
1_555
A
HOH
53
D
HOH
16
6_555
A
HOH
67
D
HOH
16
1_555
A
DC
6
A
DC
6
6
1_555
A
HOH
11
D
HOH
6
1_555
A
HOH
13
D
HOH
6
4_554
A
HOH
16
D
HOH
6
4_554
A
HOH
19
D
HOH
6
1_555
A
HOH
20
D
HOH
6
1_555
91
P 41 2 2