0.038023
0.000000
0.000000
0.000000
0.019238
0.000000
0.000000
0.000000
0.014908
0.00000
0.00000
0.00000
Smith, C.K.
Brannigan, J.A.
Moore, M.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
26.300
51.980
67.080
C2 H3 O2 -1
59.044
ACETATE ION
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
H2 O
18.015
WATER
non-polymer
Na 1
22.990
SODIUM ION
non-polymer
C39 H49 N O16
787.803
NOGALAMYCIN
non-polymer
C10 H26 N4
202.340
SPERMINE
non-polymer
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
263
237
258
10.1006/jmbi.1996.0572
8913304
Factors affecting DNA sequence selectivity of nogalamycin intercalation: the crystal structure of d(TGTACA)2-nogalamycin2.
1996
US
Biochemistry
BICHAW
0033
0006-2960
34
415
425
DNA-Nogalamycin Interactions: The Crystal Structure of d(TGATCA) Complexed with Nogalamycin
1995
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
52
299
314
DNA-Drug Refinement: A Comparison of the Programs NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, Using the Low Temperature d(TGATCA)-Nogalamycin Structure
1996
10.2210/pdb258d/pdb
pdb_0000258d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277.00
1
IMAGE PLATE
1994-07-01
HENDRIX-LENTFER
M
x-ray
1
1.0
X31
EMBL/DESY, HAMBURG
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X31
1808.229
DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
4
syn
polymer
787.803
NOGALAMYCIN
4
syn
non-polymer
202.340
SPERMINE
1
syn
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
59.044
ACETATE ION
2
syn
non-polymer
18.015
water
97
nat
water
no
no
(DT)(DG)(DT)(DA)(DC)(DA)
TGTACA
A,B,C,D
polydeoxyribonucleotide
n
n
n
n
n
n
3.17
61.19
VAPOR DIFFUSION, SITTING DROP
6.50
pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
277.00
WATER
1
MPD
1
SPERMINE
1
NA CACODYLATE
1
MG ACETATE
1
WATER
2
MPD
2
14.235
1
20
A
1
B
12
-2.121
A_DT1:DA12_B
1
2.794
-0.117
-0.200
-0.087
-26.477
1
19
A
2
B
11
-0.258
A_DG2:DC11_B
2
6.742
-0.184
-0.533
-0.067
-4.181
1
20
A
3
B
10
3.166
A_DT3:DA10_B
3
2.292
-0.023
0.222
-0.092
0.765
1
20
A
4
B
9
1.413
A_DA4:DT9_B
4
1.331
0.048
0.101
-0.117
23.313
1
19
A
5
B
8
0.502
A_DC5:DG8_B
5
4.880
0.290
-0.328
-0.068
-11.202
1
20
A
6
B
7
1.670
A_DA6:DT7_B
6
-0.667
-0.203
-0.042
-0.120
16.431
1
20
C
13
D
24
-2.891
C_DT13:DA24_D
7
3.961
-0.115
-0.101
-0.046
-26.328
1
19
C
14
D
23
0.277
C_DG14:DC23_D
8
8.544
-0.338
-0.554
-0.081
0.438
1
20
C
15
D
22
4.658
C_DT15:DA22_D
9
3.632
0.000
0.078
-0.101
3.075
1
20
C
16
D
21
1.546
C_DA16:DT21_D
10
5.362
0.062
0.022
-0.164
25.099
1
19
C
17
D
20
-0.280
C_DC17:DG20_D
11
7.588
0.260
-0.383
-0.061
-17.808
1
20
C
18
D
19
-2.672
C_DA18:DT19_D
12
2.646
0.164
-0.189
-0.147
7.301
38.479
A
A
1
2
1.594
B
B
12
11
7.269
1.038
1.051
0.435
AA_DT1DG2:DC11DA12_BB
1
10.405
-15.974
37.083
0.368
1.340
2.882
27.053
A
A
2
3
7.569
B
B
11
10
2.949
3.505
-0.259
-0.243
AA_DG2DT3:DA10DC11_BB
2
-5.781
12.486
26.210
-1.325
-0.775
3.276
36.455
A
A
3
4
-7.289
B
B
10
9
3.218
-4.548
-0.028
-0.701
AA_DT3DA4:DT9DA10_BB
3
1.127
-1.805
36.163
-0.492
0.200
2.904
26.743
A
A
4
5
9.788
B
B
9
8
2.992
4.497
0.157
-0.277
AA_DA4DC5:DG8DT9_BB
4
2.994
-6.516
26.201
-1.663
0.368
7.074
34.144
A
A
5
6
-1.518
B
B
8
7
7.034
-0.873
-1.398
0.293
AA_DC5DA6:DT7DG8_BB
5
-12.131
21.098
31.965
0.808
-1.910
7.298
36.098
C
C
13
14
-2.083
D
D
24
23
7.267
-1.274
1.154
0.195
CC_DT13DG14:DC23DA24_DD
6
10.044
-16.415
34.695
0.724
1.369
2.707
27.804
C
C
14
15
15.140
D
D
23
22
2.869
7.142
-0.296
-0.262
CC_DG14DT15:DA22DC23_DD
7
-5.829
12.355
26.259
-2.051
-0.613
3.155
37.611
C
C
15
16
-0.478
D
D
22
21
3.151
-0.308
-0.078
-0.668
CC_DT15DA16:DT21DA22_DD
8
0.435
-0.675
37.607
-0.998
0.175
2.885
27.261
C
C
16
17
12.101
D
D
21
20
2.981
5.645
0.416
-0.303
CC_DA16DC17:DG20DT21_DD
9
3.791
-8.126
26.415
-1.929
-0.018
7.347
36.671
C
C
17
18
-5.784
D
D
20
19
7.326
-3.616
-1.122
0.309
CC_DC17DA18:DT19DG20_DD
10
-6.383
10.210
35.955
1.614
-0.198
database_2
diffrn_source
pdbx_initial_refinement_model
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
1996-06-20
1
1
2008-05-22
1
2
2011-07-13
1
3
2023-08-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
NDB
Y
NDB
1996-05-12
REL
REL
NGM
NOGALAMYCIN
SPM
SPERMINE
NA
SODIUM ION
ACT
ACETATE ION
HOH
water
182D
NDB ENTRY DDF049 (PDB: 182D)
PDB
experimental model
NGM
26
2
NGM
NGM
26
A
SPM
29
3
SPM
SPM
29
A
NGM
25
2
NGM
NGM
25
B
NA
30
4
NA
NA
30
B
ACT
31
5
ACT
ACT
31
B
ACT
32
5
ACT
ACT
32
B
NGM
28
2
NGM
NGM
28
C
NGM
27
2
NGM
NGM
27
D
HOH
32
6
HOH
HOH
32
A
HOH
34
6
HOH
HOH
34
A
HOH
39
6
HOH
HOH
39
A
HOH
44
6
HOH
HOH
44
A
HOH
48
6
HOH
HOH
48
A
HOH
49
6
HOH
HOH
49
A
HOH
57
6
HOH
HOH
57
A
HOH
58
6
HOH
HOH
58
A
HOH
59
6
HOH
HOH
59
A
HOH
60
6
HOH
HOH
60
A
HOH
61
6
HOH
HOH
61
A
HOH
64
6
HOH
HOH
64
A
HOH
65
6
HOH
HOH
65
A
HOH
72
6
HOH
HOH
72
A
HOH
77
6
HOH
HOH
77
A
HOH
87
6
HOH
HOH
87
A
HOH
92
6
HOH
HOH
92
A
HOH
93
6
HOH
HOH
93
A
HOH
94
6
HOH
HOH
94
A
HOH
99
6
HOH
HOH
99
A
HOH
105
6
HOH
HOH
105
A
HOH
110
6
HOH
HOH
110
A
HOH
112
6
HOH
HOH
112
A
HOH
114
6
HOH
HOH
114
A
HOH
120
6
HOH
HOH
120
A
HOH
35
6
HOH
HOH
35
B
HOH
38
6
HOH
HOH
38
B
HOH
43
6
HOH
HOH
43
B
HOH
46
6
HOH
HOH
46
B
HOH
47
6
HOH
HOH
47
B
HOH
52
6
HOH
HOH
52
B
HOH
56
6
HOH
HOH
56
B
HOH
62
6
HOH
HOH
62
B
HOH
69
6
HOH
HOH
69
B
HOH
70
6
HOH
HOH
70
B
HOH
76
6
HOH
HOH
76
B
HOH
81
6
HOH
HOH
81
B
HOH
82
6
HOH
HOH
82
B
HOH
84
6
HOH
HOH
84
B
HOH
88
6
HOH
HOH
88
B
HOH
91
6
HOH
HOH
91
B
HOH
95
6
HOH
HOH
95
B
HOH
96
6
HOH
HOH
96
B
HOH
100
6
HOH
HOH
100
B
HOH
106
6
HOH
HOH
106
B
HOH
115
6
HOH
HOH
115
B
HOH
119
6
HOH
HOH
119
B
HOH
121
6
HOH
HOH
121
B
HOH
122
6
HOH
HOH
122
B
HOH
123
6
HOH
HOH
123
B
HOH
128
6
HOH
HOH
128
B
HOH
33
6
HOH
HOH
33
C
HOH
36
6
HOH
HOH
36
C
HOH
42
6
HOH
HOH
42
C
HOH
51
6
HOH
HOH
51
C
HOH
54
6
HOH
HOH
54
C
HOH
55
6
HOH
HOH
55
C
HOH
63
6
HOH
HOH
63
C
HOH
66
6
HOH
HOH
66
C
HOH
68
6
HOH
HOH
68
C
HOH
71
6
HOH
HOH
71
C
HOH
74
6
HOH
HOH
74
C
HOH
75
6
HOH
HOH
75
C
HOH
79
6
HOH
HOH
79
C
HOH
80
6
HOH
HOH
80
C
HOH
83
6
HOH
HOH
83
C
HOH
85
6
HOH
HOH
85
C
HOH
86
6
HOH
HOH
86
C
HOH
89
6
HOH
HOH
89
C
HOH
101
6
HOH
HOH
101
C
HOH
104
6
HOH
HOH
104
C
HOH
111
6
HOH
HOH
111
C
HOH
113
6
HOH
HOH
113
C
HOH
116
6
HOH
HOH
116
C
HOH
117
6
HOH
HOH
117
C
HOH
124
6
HOH
HOH
124
C
HOH
126
6
HOH
HOH
126
C
HOH
127
6
HOH
HOH
127
C
HOH
37
6
HOH
HOH
37
D
HOH
40
6
HOH
HOH
40
D
HOH
41
6
HOH
HOH
41
D
HOH
45
6
HOH
HOH
45
D
HOH
50
6
HOH
HOH
50
D
HOH
53
6
HOH
HOH
53
D
HOH
67
6
HOH
HOH
67
D
HOH
73
6
HOH
HOH
73
D
HOH
78
6
HOH
HOH
78
D
HOH
90
6
HOH
HOH
90
D
HOH
97
6
HOH
HOH
97
D
HOH
98
6
HOH
HOH
98
D
HOH
102
6
HOH
HOH
102
D
HOH
103
6
HOH
HOH
103
D
HOH
107
6
HOH
HOH
107
D
HOH
108
6
HOH
HOH
108
D
HOH
109
6
HOH
HOH
109
D
HOH
118
6
HOH
HOH
118
D
HOH
125
6
HOH
HOH
125
D
T
1
n
1
DT
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
T
7
n
1
DT
7
B
G
8
n
2
DG
8
B
T
9
n
3
DT
9
B
A
10
n
4
DA
10
B
C
11
n
5
DC
11
B
A
12
n
6
DA
12
B
T
13
n
1
DT
13
C
G
14
n
2
DG
14
C
T
15
n
3
DT
15
C
A
16
n
4
DA
16
C
C
17
n
5
DC
17
C
A
18
n
6
DA
18
C
T
19
n
1
DT
19
D
G
20
n
2
DG
20
D
T
21
n
3
DT
21
D
A
22
n
4
DA
22
D
C
23
n
5
DC
23
D
A
24
n
6
DA
24
D
0.1800000
0.1920000
0.1760000
0.1880000
0.2390000
0.2370000
1235.0
1235.0
10.00
10.000
12358
author_defined_assembly
2
dimeric
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
C
C9
NGM
28
WRONG HAND
1
-5.65
0.80
109.40
103.75
A
A
A
O5'
C5'
C4'
DT
DT
DT
1
1
1
N
1
8.72
0.90
103.10
111.82
A
A
A
C4'
C3'
C2'
DT
DT
DT
1
1
1
N
1
3.14
0.30
108.30
111.44
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
7.15
0.60
119.90
127.05
A
A
A
N3
C4
O4
DT
DT
DT
1
1
1
N
1
-6.10
0.70
124.90
118.80
A
A
A
C5
C4
O4
DT
DT
DT
1
1
1
N
1
-8.14
0.80
109.40
101.26
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
6.86
0.90
103.10
109.96
A
A
A
C4'
C3'
C2'
DG
DG
DG
2
2
2
N
1
2.85
0.30
108.30
111.15
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.64
0.60
128.60
132.24
A
A
A
C5
C6
O6
DG
DG
DG
2
2
2
N
1
13.88
1.20
119.70
133.58
A
A
A
C3'
O3'
P
DG
DG
DT
2
2
3
Y
1
15.99
1.50
119.60
135.59
A
A
A
OP1
P
OP2
DT
DT
DT
3
3
3
N
1
-6.59
0.80
109.40
102.81
A
A
A
O5'
C5'
C4'
DT
DT
DT
3
3
3
N
1
-13.46
1.60
120.90
107.44
A
A
A
P
O5'
C5'
DT
DT
DT
3
3
3
N
1
8.15
0.90
103.10
111.25
A
A
A
C4'
C3'
C2'
DT
DT
DT
3
3
3
N
1
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
10.56
1.20
119.70
130.26
A
A
A
C3'
O3'
P
DT
DT
DA
3
3
4
Y
1
16.32
1.50
119.60
135.92
A
A
A
OP1
P
OP2
DA
DA
DA
4
4
4
N
1
-8.28
0.80
109.40
101.12
A
A
A
O5'
C5'
C4'
DA
DA
DA
4
4
4
N
1
6.99
0.90
103.10
110.09
A
A
A
C4'
C3'
C2'
DA
DA
DA
4
4
4
N
1
11.09
1.20
119.70
130.79
A
A
A
C3'
O3'
P
DA
DA
DC
4
4
5
Y
1
20.41
1.50
119.60
140.01
A
A
A
OP1
P
OP2
DC
DC
DC
5
5
5
N
1
-7.69
0.80
109.40
101.71
A
A
A
O5'
C5'
C4'
DC
DC
DC
5
5
5
N
1
5.77
0.90
103.10
108.87
A
A
A
C4'
C3'
C2'
DC
DC
DC
5
5
5
N
1
7.04
0.30
108.30
115.34
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.40
0.40
120.30
122.70
A
A
A
C6
N1
C2
DC
DC
DC
5
5
5
N
1
-5.27
0.50
119.90
114.63
A
A
A
C2
N3
C4
DC
DC
DC
5
5
5
N
1
4.66
0.40
121.90
126.56
A
A
A
N3
C4
C5
DC
DC
DC
5
5
5
N
1
-6.86
0.80
109.40
102.54
A
A
A
O5'
C5'
C4'
DA
DA
DA
6
6
6
N
1
7.30
0.90
103.10
110.40
A
A
A
C4'
C3'
C2'
DA
DA
DA
6
6
6
N
1
-4.08
0.50
129.30
125.22
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
5.20
0.50
110.60
115.80
A
A
A
C2
N3
C4
DA
DA
DA
6
6
6
N
1
-2.96
0.40
105.80
102.84
A
A
A
N9
C4
C5
DA
DA
DA
6
6
6
N
1
5.38
0.80
127.40
132.78
A
A
A
N3
C4
N9
DA
DA
DA
6
6
6
N
1
-5.84
0.80
123.70
117.86
A
A
A
C5
C6
N6
DA
DA
DA
6
6
6
N
1
-6.67
0.80
109.40
102.73
B
B
B
O5'
C5'
C4'
DT
DT
DT
7
7
7
N
1
-2.53
0.40
104.50
101.97
B
B
B
O4'
C4'
C3'
DT
DT
DT
7
7
7
N
1
5.47
0.90
103.10
108.57
B
B
B
C4'
C3'
C2'
DT
DT
DT
7
7
7
N
1
-5.03
0.60
127.20
122.17
B
B
B
C2
N3
C4
DT
DT
DT
7
7
7
N
1
-4.65
0.60
123.70
119.05
B
B
B
C5
C6
N1
DT
DT
DT
7
7
7
N
1
14.60
1.20
119.70
134.30
B
B
B
C3'
O3'
P
DT
DT
DG
7
7
8
Y
1
10.76
1.50
119.60
130.36
B
B
B
OP1
P
OP2
DG
DG
DG
8
8
8
N
1
-7.18
0.80
109.40
102.22
B
B
B
O5'
C5'
C4'
DG
DG
DG
8
8
8
N
1
7.27
0.90
103.10
110.37
B
B
B
C4'
C3'
C2'
DG
DG
DG
8
8
8
N
1
3.32
0.30
108.30
111.62
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
-6.08
0.60
125.10
119.02
B
B
B
C6
N1
C2
DG
DG
DG
8
8
8
N
1
4.06
0.50
111.50
115.56
B
B
B
C5
C6
N1
DG
DG
DG
8
8
8
N
1
-6.47
0.90
116.20
109.73
B
B
B
N1
C2
N2
DG
DG
DG
8
8
8
N
1
-5.86
0.60
119.90
114.04
B
B
B
N1
C6
O6
DG
DG
DG
8
8
8
N
1
14.70
1.20
119.70
134.40
B
B
B
C3'
O3'
P
DG
DG
DT
8
8
9
Y
1
11.56
1.50
119.60
131.16
B
B
B
OP1
P
OP2
DT
DT
DT
9
9
9
N
1
-9.00
0.80
109.40
100.40
B
B
B
O5'
C5'
C4'
DT
DT
DT
9
9
9
N
1
6.94
0.90
103.10
110.04
B
B
B
C4'
C3'
C2'
DT
DT
DT
9
9
9
N
1
2.46
0.30
108.30
110.76
B
B
B
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
10.11
1.20
119.70
129.81
B
B
B
C3'
O3'
P
DT
DT
DA
9
9
10
Y
1
18.36
1.50
119.60
137.96
B
B
B
OP1
P
OP2
DA
DA
DA
10
10
10
N
1
-7.70
0.80
109.40
101.70
B
B
B
O5'
C5'
C4'
DA
DA
DA
10
10
10
N
1
6.91
0.90
103.10
110.01
B
B
B
C4'
C3'
C2'
DA
DA
DA
10
10
10
N
1
4.03
0.60
118.60
122.63
B
B
B
C6
N1
C2
DA
DA
DA
10
10
10
N
1
25.58
1.50
119.60
145.18
B
B
B
OP1
P
OP2
DC
DC
DC
11
11
11
N
1
-8.81
0.80
109.40
100.59
B
B
B
O5'
C5'
C4'
DC
DC
DC
11
11
11
N
1
7.08
0.90
103.10
110.18
B
B
B
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
1
8.33
0.30
108.30
116.63
B
B
B
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
4.38
0.70
118.00
122.38
B
B
B
N3
C4
N4
DC
DC
DC
11
11
11
N
1
-4.54
0.70
120.20
115.66
B
B
B
C5
C4
N4
DC
DC
DC
11
11
11
N
1
6.00
0.90
103.10
109.10
B
B
B
C4'
C3'
C2'
DA
DA
DA
12
12
12
N
1
3.90
0.60
118.60
122.50
B
B
B
C6
N1
C2
DA
DA
DA
12
12
12
N
1
-5.78
0.50
110.60
104.82
B
B
B
C2
N3
C4
DA
DA
DA
12
12
12
N
1
4.20
0.50
117.00
121.20
B
B
B
C4
C5
C6
DA
DA
DA
12
12
12
N
1
-6.02
0.50
117.70
111.68
B
B
B
C5
C6
N1
DA
DA
DA
12
12
12
N
1
-4.75
0.70
132.30
127.55
B
B
B
C6
C5
N7
DA
DA
DA
12
12
12
N
1
-5.33
0.80
109.40
104.07
C
C
C
O5'
C5'
C4'
DT
DT
DT
13
13
13
N
1
6.81
0.90
103.10
109.91
C
C
C
C4'
C3'
C2'
DT
DT
DT
13
13
13
N
1
3.80
0.30
108.30
112.10
C
C
C
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
10.81
1.50
119.60
130.41
C
C
C
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-7.42
0.80
109.40
101.98
C
C
C
O5'
C5'
C4'
DG
DG
DG
14
14
14
N
1
6.71
0.90
103.10
109.81
C
C
C
C4'
C3'
C2'
DG
DG
DG
14
14
14
N
1
3.32
0.30
108.30
111.62
C
C
C
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
15.17
1.20
119.70
134.87
C
C
C
C3'
O3'
P
DG
DG
DT
14
14
15
Y
1
16.94
1.50
119.60
136.54
C
C
C
OP1
P
OP2
DT
DT
DT
15
15
15
N
1
-8.88
0.80
109.40
100.52
C
C
C
O5'
C5'
C4'
DT
DT
DT
15
15
15
N
1
7.35
0.90
103.10
110.45
C
C
C
C4'
C3'
C2'
DT
DT
DT
15
15
15
N
1
13.43
1.20
119.70
133.13
C
C
C
C3'
O3'
P
DT
DT
DA
15
15
16
Y
1
17.92
1.50
119.60
137.52
C
C
C
OP1
P
OP2
DA
DA
DA
16
16
16
N
1
-11.34
0.80
109.40
98.06
C
C
C
O5'
C5'
C4'
DA
DA
DA
16
16
16
N
1
7.46
0.90
103.10
110.56
C
C
C
C4'
C3'
C2'
DA
DA
DA
16
16
16
N
1
-3.54
0.50
129.30
125.76
C
C
C
N1
C2
N3
DA
DA
DA
16
16
16
N
1
26.66
1.50
119.60
146.26
C
C
C
OP1
P
OP2
DC
DC
DC
17
17
17
N
1
-7.77
0.80
109.40
101.63
C
C
C
O5'
C5'
C4'
DC
DC
DC
17
17
17
N
1
6.57
0.90
103.10
109.67
C
C
C
C4'
C3'
C2'
DC
DC
DC
17
17
17
N
1
8.23
0.30
108.30
116.53
C
C
C
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
3.47
0.50
119.90
123.37
C
C
C
C2
N3
C4
DC
DC
DC
17
17
17
N
1
-7.59
0.80
109.40
101.81
C
C
C
O5'
C5'
C4'
DA
DA
DA
18
18
18
N
1
6.27
0.90
103.10
109.37
C
C
C
C4'
C3'
C2'
DA
DA
DA
18
18
18
N
1
-3.20
0.50
110.60
107.40
C
C
C
C2
N3
C4
DA
DA
DA
18
18
18
N
1
-5.39
0.80
109.40
104.01
D
D
D
O5'
C5'
C4'
DT
DT
DT
19
19
19
N
1
7.90
0.90
103.10
111.00
D
D
D
C4'
C3'
C2'
DT
DT
DT
19
19
19
N
1
5.66
0.30
108.30
113.96
D
D
D
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
-5.11
0.80
123.10
117.99
D
D
D
N1
C2
O2
DT
DT
DT
19
19
19
N
1
4.50
0.60
122.30
126.80
D
D
D
N3
C2
O2
DT
DT
DT
19
19
19
N
1
21.22
1.50
119.60
140.82
D
D
D
OP1
P
OP2
DG
DG
DG
20
20
20
N
1
-9.63
0.80
109.40
99.77
D
D
D
O5'
C5'
C4'
DG
DG
DG
20
20
20
N
1
7.26
0.90
103.10
110.36
D
D
D
C4'
C3'
C2'
DG
DG
DG
20
20
20
N
1
2.59
0.30
108.30
110.89
D
D
D
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
-5.28
0.50
111.90
106.62
D
D
D
C2
N3
C4
DG
DG
DG
20
20
20
N
1
-3.67
0.50
111.50
107.83
D
D
D
C5
C6
N1
DG
DG
DG
20
20
20
N
1
4.01
0.50
113.10
117.11
D
D
D
N7
C8
N9
DG
DG
DG
20
20
20
N
1
-3.27
0.40
106.40
103.13
D
D
D
C8
N9
C4
DG
DG
DG
20
20
20
N
1
10.95
1.20
119.70
130.65
D
D
D
C3'
O3'
P
DG
DG
DT
20
20
21
Y
1
14.58
1.50
119.60
134.18
D
D
D
OP1
P
OP2
DT
DT
DT
21
21
21
N
1
-5.34
0.80
109.40
104.06
D
D
D
O5'
C5'
C4'
DT
DT
DT
21
21
21
N
1
7.25
0.90
103.10
110.35
D
D
D
C4'
C3'
C2'
DT
DT
DT
21
21
21
N
1
2.29
0.30
108.30
110.59
D
D
D
O4'
C1'
N1
DT
DT
DT
21
21
21
N
1
17.92
1.50
119.60
137.52
D
D
D
OP1
P
OP2
DA
DA
DA
22
22
22
N
1
-6.05
0.80
109.40
103.35
D
D
D
O5'
C5'
C4'
DA
DA
DA
22
22
22
N
1
25.17
1.50
119.60
144.77
D
D
D
OP1
P
OP2
DC
DC
DC
23
23
23
N
1
-8.72
0.80
109.40
100.68
D
D
D
O5'
C5'
C4'
DC
DC
DC
23
23
23
N
1
10.04
0.30
108.30
118.34
D
D
D
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
6.47
0.60
118.90
125.37
D
D
D
N1
C2
O2
DC
DC
DC
23
23
23
N
1
-4.93
0.70
121.90
116.97
D
D
D
N3
C2
O2
DC
DC
DC
23
23
23
N
1
17.42
1.50
119.60
137.02
D
D
D
OP1
P
OP2
DA
DA
DA
24
24
24
N
1
5.73
0.90
103.10
108.83
D
D
D
C4'
C3'
C2'
DA
DA
DA
24
24
24
N
1
-4.29
0.50
129.30
125.01
D
D
D
N1
C2
N3
DA
DA
DA
24
24
24
N
1
A
A
C5'
C4'
DT
DT
1
1
0.045
0.007
1.512
1.557
N
1
A
A
C4'
C3'
DT
DT
1
1
-0.064
0.010
1.521
1.457
N
1
A
A
C5'
C4'
DG
DG
2
2
0.054
0.007
1.512
1.566
N
1
A
A
C2'
C1'
DG
DG
2
2
0.061
0.010
1.519
1.580
N
1
A
A
P
O5'
DT
DT
3
3
0.086
0.010
1.593
1.679
N
1
A
A
C5
C7
DT
DT
3
3
0.038
0.006
1.496
1.534
N
1
A
A
P
O5'
DA
DA
4
4
0.069
0.010
1.593
1.662
N
1
A
A
C5'
C4'
DA
DA
4
4
0.056
0.007
1.512
1.568
N
1
A
A
O3'
P
DA
DC
4
5
0.083
0.012
1.607
1.690
Y
1
A
A
P
O5'
DC
DC
5
5
0.066
0.010
1.593
1.659
N
1
A
A
C5'
C4'
DC
DC
5
5
0.050
0.007
1.512
1.562
N
1
A
A
C4'
C3'
DC
DC
5
5
-0.065
0.010
1.521
1.456
N
1
A
A
C2'
C1'
DC
DC
5
5
0.078
0.010
1.519
1.597
N
1
A
A
O3'
P
DC
DA
5
6
0.079
0.012
1.607
1.686
Y
1
A
A
C6
N1
DA
DA
6
6
-0.050
0.007
1.351
1.301
N
1
B
B
P
O5'
DG
DG
8
8
0.066
0.010
1.593
1.659
N
1
B
B
C5'
C4'
DG
DG
8
8
0.055
0.007
1.512
1.567
N
1
B
B
O3'
P
DA
DC
10
11
0.081
0.012
1.607
1.688
Y
1
B
B
P
O5'
DC
DC
11
11
0.070
0.010
1.593
1.663
N
1
B
B
C5'
C4'
DC
DC
11
11
0.057
0.007
1.512
1.569
N
1
B
B
C4'
C3'
DC
DC
11
11
-0.062
0.010
1.521
1.459
N
1
B
B
C2'
C1'
DC
DC
11
11
0.081
0.010
1.519
1.600
N
1
C
C
C5'
C4'
DT
DT
13
13
0.046
0.007
1.512
1.558
N
1
C
C
C4'
C3'
DT
DT
13
13
-0.068
0.010
1.521
1.453
N
1
C
C
C5'
C4'
DG
DG
14
14
0.048
0.007
1.512
1.560
N
1
C
C
O3'
P
DG
DT
14
15
0.073
0.012
1.607
1.680
Y
1
C
C
C4'
C3'
DT
DT
15
15
-0.065
0.010
1.521
1.456
N
1
C
C
C5'
C4'
DA
DA
16
16
0.050
0.007
1.512
1.562
N
1
C
C
O3'
P
DA
DC
16
17
0.087
0.012
1.607
1.694
Y
1
C
C
P
O5'
DC
DC
17
17
0.081
0.010
1.593
1.674
N
1
C
C
C5'
C4'
DC
DC
17
17
0.053
0.007
1.512
1.565
N
1
C
C
C4'
C3'
DC
DC
17
17
-0.073
0.010
1.521
1.448
N
1
C
C
C2'
C1'
DC
DC
17
17
0.079
0.010
1.519
1.598
N
1
C
C
O4'
C4'
DC
DC
17
17
0.055
0.009
1.449
1.504
N
1
C
C
C5'
C4'
DA
DA
18
18
0.054
0.007
1.512
1.566
N
1
C
C
C4'
C3'
DA
DA
18
18
-0.065
0.010
1.521
1.456
N
1
D
D
C5'
C4'
DT
DT
19
19
0.047
0.007
1.512
1.559
N
1
D
D
C4'
C3'
DT
DT
19
19
-0.063
0.010
1.521
1.458
N
1
D
D
O3'
P
DT
DG
19
20
0.077
0.012
1.607
1.684
Y
1
D
D
P
O5'
DG
DG
20
20
0.066
0.010
1.593
1.659
N
1
D
D
C5'
C4'
DG
DG
20
20
0.058
0.007
1.512
1.570
N
1
D
D
C2'
C1'
DG
DG
20
20
0.067
0.010
1.519
1.586
N
1
D
D
P
O5'
DA
DA
22
22
0.072
0.010
1.593
1.665
N
1
D
D
C4'
C3'
DA
DA
22
22
-0.063
0.010
1.521
1.458
N
1
D
D
P
O5'
DC
DC
23
23
0.066
0.010
1.593
1.659
N
1
D
D
C5'
C4'
DC
DC
23
23
0.050
0.007
1.512
1.562
N
1
D
D
C2'
C1'
DC
DC
23
23
0.085
0.010
1.519
1.604
N
1
D
D
O3'
P
DC
DA
23
24
0.088
0.012
1.607
1.695
Y
21.78
ESTIMATED COORDINATE ERROR (A) : 0.12A
0.2370000
0.1880000
0.1920000
0.1880000
1.580
10.690
3310
1235
12358
12358
12049
10.000
94.000
1
FREE R-VALUE
0.000
MOLECULAR REPLACEMENT
NDB ENTRY DDF049 (PDB: 182D)
TAYLOR AND KENNARD
BABINET'S PRINCIPLE
TR
isotropic
TR
isotropic
1.580
10.690
97
824
247
480
0
0.015
0.023
0.089
0.091
0.004
0.022
0.057
fix
fix
1.580
10.690
258D
13148
1.000
0.0460000
1
6.300
94.000
0.1960000
1.580
1.660
3.600
69.50
phasing
AMoRE
refinement
SHELXL-93
data reduction
DENZO
data scaling
CCP4
FACTORS AFFECTING SEQUENCE SELECTIVITY ON NOGALAMYCIN INTERCALATION: THE CRYSTAL STRUCTURE OF D(TGTACA)-NOGALAMYCIN
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
4
N
N
5
N
N
5
N
N
2
N
N
2
N
N
6
N
N
6
N
N
6
N
N
6
N
N
metalc
2.684
B
DA
12
B
N7
DA
6
1_555
B
NA
30
H
NA
NA
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
12
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
12
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
11
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
11
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
11
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
10
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
10
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
9
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
9
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
7
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
7
B
O4
DT
1
1_555
hydrog
WATSON-CRICK
C
DT
13
C
N3
DT
1
1_555
D
DA
24
D
N1
DA
6
1_555
hydrog
WATSON-CRICK
C
DT
13
C
O4
DT
1
1_555
D
DA
24
D
N6
DA
6
1_555
hydrog
WATSON-CRICK
C
DG
14
C
N1
DG
2
1_555
D
DC
23
D
N3
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
14
C
N2
DG
2
1_555
D
DC
23
D
O2
DC
5
1_555
hydrog
WATSON-CRICK
C
DG
14
C
O6
DG
2
1_555
D
DC
23
D
N4
DC
5
1_555
hydrog
WATSON-CRICK
C
DT
15
C
N3
DT
3
1_555
D
DA
22
D
N1
DA
4
1_555
hydrog
WATSON-CRICK
C
DT
15
C
O4
DT
3
1_555
D
DA
22
D
N6
DA
4
1_555
hydrog
WATSON-CRICK
C
DA
16
C
N1
DA
4
1_555
D
DT
21
D
N3
DT
3
1_555
hydrog
WATSON-CRICK
C
DA
16
C
N6
DA
4
1_555
D
DT
21
D
O4
DT
3
1_555
hydrog
WATSON-CRICK
C
DC
17
C
N3
DC
5
1_555
D
DG
20
D
N1
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
17
C
N4
DC
5
1_555
D
DG
20
D
O6
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
17
C
O2
DC
5
1_555
D
DG
20
D
N2
DG
2
1_555
hydrog
WATSON-CRICK
C
DA
18
C
N1
DA
6
1_555
D
DT
19
D
N3
DT
1
1_555
hydrog
WATSON-CRICK
C
DA
18
C
N6
DA
6
1_555
D
DT
19
D
O4
DT
1
1_555
DNA
B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA
258D
PDB
1
258D
1
6
258D
1
6
258D
A
1
1
6
7
12
258D
7
12
258D
B
1
1
6
13
18
258D
13
18
258D
C
1
1
6
19
24
258D
19
24
258D
D
1
1
6
BINDING SITE FOR RESIDUE NGM B 25
B
NGM
25
Software
16
BINDING SITE FOR RESIDUE NGM A 26
A
NGM
26
Software
14
BINDING SITE FOR RESIDUE NGM D 27
D
NGM
27
Software
10
BINDING SITE FOR RESIDUE NGM C 28
C
NGM
28
Software
15
BINDING SITE FOR RESIDUE SPM A 29
A
SPM
29
Software
8
BINDING SITE FOR RESIDUE NA B 30
B
NA
30
Software
3
BINDING SITE FOR RESIDUE ACT B 31
B
ACT
31
Software
5
BINDING SITE FOR RESIDUE ACT B 32
B
ACT
32
Software
4
A
DT
1
A
DT
1
16
3_645
A
DC
5
A
DC
5
16
1_555
A
DA
6
A
DA
6
16
1_555
A
NGM
26
E
NGM
16
3_645
B
DT
7
B
DT
1
16
1_555
B
DG
8
B
DG
2
16
1_555
B
DT
9
B
DT
3
16
1_555
B
DA
10
B
DA
4
16
1_555
B
HOH
46
N
HOH
16
1_555
B
HOH
81
N
HOH
16
1_555
B
HOH
82
N
HOH
16
1_555
B
HOH
84
N
HOH
16
1_555
B
HOH
95
N
HOH
16
1_555
B
HOH
96
N
HOH
16
1_555
C
DA
18
C
DA
6
16
1_555
D
DA
24
D
DA
6
16
1_655
A
DT
1
A
DT
1
14
1_555
A
DG
2
A
DG
2
14
1_555
A
DT
3
A
DT
3
14
1_555
A
DA
4
A
DA
4
14
1_555
A
SPM
29
F
SPM
14
1_555
A
HOH
44
M
HOH
14
1_555
A
HOH
64
M
HOH
14
1_555
A
HOH
65
M
HOH
14
1_555
A
HOH
77
M
HOH
14
1_555
A
HOH
94
M
HOH
14
1_555
B
DC
11
B
DC
5
14
1_555
B
DA
12
B
DA
6
14
1_555
B
NGM
25
G
NGM
14
3_655
B
ACT
32
J
ACT
14
1_555
A
SPM
29
F
SPM
10
4_456
C
DC
17
C
DC
5
10
1_555
C
DA
18
C
DA
6
10
1_555
D
DT
19
D
DT
1
10
1_555
D
DG
20
D
DG
2
10
1_555
D
DT
21
D
DT
3
10
1_555
D
DA
22
D
DA
4
10
1_555
D
HOH
73
P
HOH
10
1_555
D
HOH
108
P
HOH
10
1_555
D
HOH
125
P
HOH
10
1_555
A
DT
1
A
DT
1
15
4_456
A
DG
2
A
DG
2
15
4_456
B
DA
12
B
DA
6
15
3_545
C
DT
13
C
DT
1
15
1_555
C
DG
14
C
DG
2
15
1_555
C
DT
15
C
DT
3
15
1_555
C
DA
16
C
DA
4
15
1_555
C
HOH
66
O
HOH
15
1_555
C
HOH
71
O
HOH
15
1_555
C
HOH
83
O
HOH
15
1_555
C
HOH
86
O
HOH
15
1_555
C
HOH
113
O
HOH
15
1_555
C
HOH
126
O
HOH
15
1_555
D
DC
23
D
DC
5
15
1_555
D
DA
24
D
DA
6
15
1_555
A
DT
1
A
DT
1
8
1_555
A
DA
6
A
DA
6
8
3_655
A
NGM
26
E
NGM
8
1_555
A
HOH
48
M
HOH
8
1_555
A
HOH
72
M
HOH
8
1_555
D
DG
20
D
DG
2
8
4_556
D
DT
21
D
DT
3
8
4_556
D
NGM
27
L
NGM
8
4_556
B
DA
12
B
DA
6
3
1_555
B
ACT
31
I
ACT
3
1_555
B
ACT
32
J
ACT
3
1_555
B
DC
11
B
DC
5
5
1_555
B
DA
12
B
DA
6
5
1_555
B
NA
30
H
NA
5
1_555
B
ACT
32
J
ACT
5
1_555
B
HOH
106
N
HOH
5
1_555
A
NGM
26
E
NGM
4
1_555
A
HOH
34
M
HOH
4
1_555
B
NA
30
H
NA
4
1_555
B
ACT
31
I
ACT
4
1_555
19
P 21 21 21