1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Tuma, J.
Connors, W.H.
Stitelman, D.H.
Richert, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H15 N3 O4
241.244
n
5'-AMINO-5'-DEOXYTHYMIDINE
DNA linking
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
C13 H11 N O5
261.230
OXOLINIC ACID
non-polymer
N
1
N
N
N
2
N
N
N
3
N
C
N
4
N
C
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
O
N
9
N
C
N
10
N
C
N
11
N
C
N
12
N
C
N
13
R
C
N
14
N
O
N
15
R
C
N
16
S
C
N
17
N
O
N
18
N
H
N
19
N
H
N
20
N
H
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
O
N
34
N
P
N
35
N
O
N
36
N
O
N
37
N
O
N
38
N
C
N
39
R
C
N
40
N
O
N
41
S
C
N
42
N
O
N
43
N
C
N
44
R
C
Y
45
N
N
Y
46
N
C
Y
47
N
N
Y
48
N
C
Y
49
N
C
N
50
N
N
Y
51
N
N
Y
52
N
C
Y
53
N
N
Y
54
N
C
N
55
N
H
N
56
N
H
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
O
N
70
N
P
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
C
N
75
R
C
N
76
N
O
N
77
S
C
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
N
N
82
N
C
N
83
N
O
N
84
N
N
N
85
N
C
N
86
N
N
N
87
N
C
N
88
N
C
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
O
N
104
N
P
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
C
N
109
R
C
N
110
N
O
N
111
S
C
N
112
N
O
N
113
N
C
N
114
R
C
Y
115
N
N
Y
116
N
C
Y
117
N
N
Y
118
N
C
N
119
N
C
N
120
N
O
N
121
N
N
N
122
N
C
N
123
N
N
N
124
N
N
Y
125
N
C
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
C
N
141
N
O
Y
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
N
146
N
O
Y
147
N
C
Y
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
N
153
N
O
N
154
N
O
N
155
N
C
N
156
N
C
N
157
N
C
N
158
N
O
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
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
doub
N
8
N
sing
N
9
N
doub
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
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
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
doub
N
37
N
sing
N
38
N
sing
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
Y
57
N
sing
Y
58
N
sing
Y
59
N
doub
N
60
N
sing
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
doub
N
66
N
sing
N
67
N
sing
Y
68
N
sing
Y
69
N
doub
N
70
N
sing
Y
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
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
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
N
97
N
doub
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
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
sing
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
Y
130
N
sing
Y
131
N
sing
Y
132
N
doub
N
133
N
sing
Y
134
N
sing
N
135
N
sing
Y
136
N
doub
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
Y
149
N
doub
Y
150
N
sing
Y
151
N
sing
N
152
N
sing
Y
153
N
sing
N
154
N
sing
N
155
N
doub
Y
156
N
sing
Y
157
N
doub
Y
158
N
sing
Y
159
N
sing
Y
160
N
doub
N
161
N
sing
Y
162
N
doub
N
163
N
sing
Y
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
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
124
4236
4246
10.1021/ja0125117
11960452
On the effect of covalently appended quinolones on termini of DNA duplexes.
2002
10.2210/pdb1kse/pdb
pdb_00001kse
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
SINGLE WAVELENGTH
M
1
1.0
Quinolone-DNA hybrid
1728.254
5'-D(*(5AT)P*GP*CP*GP*CP*A)-3'
2
syn
polymer
261.230
OXOLINIC ACID
2
syn
non-polymer
no
yes
(5AT)(DG)(DC)(DG)(DC)(DA)
TGCGCA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
-7.550
1
19
A
2
B
5
-2.740
A_DG2:DC5_B
1
-7.786
-1.510
0.378
-0.658
-5.593
1
19
A
3
B
4
-1.682
A_DC3:DG4_B
2
-5.073
-0.157
0.390
-0.184
7.058
1
19
A
4
B
3
-1.487
A_DG4:DC3_B
3
-2.748
0.001
0.439
-0.194
12.265
1
19
A
5
B
2
-1.904
A_DC5:DG2_B
4
-12.002
0.957
-0.004
-0.427
3.159
47.332
A
A
2
3
12.647
B
B
5
4
3.238
10.060
0.100
0.112
AA_DG2DC3:DG4DC5_BB
1
-5.886
7.399
45.955
-0.673
-0.599
2.924
33.276
A
A
3
4
10.548
B
B
4
3
2.831
6.009
0.143
0.786
AA_DC3DG4:DC3DG4_BB
2
-0.282
0.495
32.743
0.484
-0.292
3.077
43.925
A
A
4
5
18.153
B
B
3
2
3.233
13.276
-0.306
0.432
AA_DG4DC5:DG2DC3_BB
3
9.785
-13.379
40.853
-0.684
1.340
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Data collection
1
0
2002-05-08
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-01-12
REL
OXI
OXOLINIC ACID
Custom synthesized by the authors
sample
closest to the average
1
2D NOESY, DQF-COSY, TOCSY
2D NOESY
165 mM Phosphate buffer(KH2PO4/K2HPO4), NaCl at pH 7 (uncorrected for deuterium effect)
7
ambient
283
K
Torsion-Angle Molecular Dynamics
analyte buffer, salt, D2O
D2O
analyte buffer, salt, H2O/D2O (85:15)
H2O/D2O (85:15)
Brunger
structure solution
CNS
1.0
Brunger
refinement
CNS
1.0
600
Bruker
DPX
T
1
2
OXI
OXI
0
A
T
1
2
OXI
OXI
0
B
T
1
n
1
5AT
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
T
1
n
1
5AT
1
B
G
2
n
2
DG
2
B
C
3
n
3
DC
3
B
G
4
n
4
DG
4
B
C
5
n
5
DC
5
B
A
6
n
6
DA
6
B
author_defined_assembly
2
dimeric
A
5AT
1
5'-AMINO-5'-DEOXYTHYMIDINE
A
5AT
1
DT
B
5AT
1
5'-AMINO-5'-DEOXYTHYMIDINE
B
5AT
1
DT
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
Solution Structure of a quinolone-capped DNA duplex
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.350
none
A
OXI
0
C
C1
OXI
1_555
A
5AT
1
A
N5'
5AT
1
1_555
covale
1.607
both
A
5AT
1
A
O3'
5AT
1
1_555
A
DG
2
A
P
DG
2
1_555
covale
1.357
none
B
OXI
0
D
C1
OXI
1_555
B
5AT
1
B
N5'
5AT
1
1_555
covale
1.611
both
B
5AT
1
B
O3'
5AT
1
1_555
B
DG
2
B
P
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
5
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
5
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
5
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
4
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
4
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
4
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
3
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
3
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
3
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
2
B
N2
DG
2
1_555
DNA
DNA, quinolone, Synthetic hybrid, disrupted terminal basepairs
1KSE
PDB
1
1KSE
1
6
1KSE
1
6
1KSE
A
1
1
6
1
6
1KSE
1
6
1KSE
B
1
1
6
BINDING SITE FOR RESIDUE OXI A 0
A
OXI
0
Software
4
BINDING SITE FOR RESIDUE OXI B 0
B
OXI
0
Software
4
A
5AT
1
A
5AT
1
4
1_555
A
DG
2
A
DG
2
4
1_555
B
DC
5
B
DC
5
4
1_555
B
DA
6
B
DA
6
4
1_555
A
DC
5
A
DC
5
4
1_555
A
DA
6
A
DA
6
4
1_555
B
5AT
1
B
5AT
1
4
1_555
B
DG
2
B
DG
2
4
1_555