1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Peterson, L.A.
Vu, C.
Hingerty, B.E.
Broyde, S.
Cosman, M.
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 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C19 H23 N6 O8 P
494.395
n
O6-[4-oxo-4-(3-pyridyl)butyl]-2'-deoxyguanosine-5'-monophosphate
DNA linking
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
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
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
H
N
141
N
H
N
142
N
H
N
143
N
H
Y
144
N
C
Y
145
N
C
Y
146
N
C
Y
147
N
N
Y
148
N
C
N
149
N
N
N
150
N
C
N
151
N
O
N
152
N
C
N
153
N
C
Y
154
N
N
N
155
N
C
Y
156
N
C
Y
157
N
C
N
158
N
P
N
159
N
O
N
160
N
O
N
161
N
O
N
162
N
C
N
163
R
C
N
164
N
O
N
165
S
C
N
166
N
O
N
167
N
C
N
168
R
C
Y
169
N
N
Y
170
N
N
Y
171
N
C
Y
172
N
C
Y
173
N
C
Y
174
N
N
Y
175
N
C
N
176
N
O
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
O
N
200
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
N
136
N
sing
N
137
N
sing
N
138
N
doub
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
doub
N
146
N
sing
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
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
Y
162
N
sing
Y
163
N
sing
Y
164
N
sing
Y
165
N
doub
N
166
N
sing
Y
167
N
doub
Y
168
N
doub
Y
169
N
sing
Y
170
N
sing
Y
171
N
sing
Y
172
N
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
Y
180
N
doub
Y
181
N
sing
Y
182
N
sing
Y
183
N
doub
Y
184
N
doub
Y
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
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
42
13134
13144
10.1021/bi035217v
14609323
Solution structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11 mer DNA duplex: evidence for formation of a base triplex.
2003
10.2210/pdb1pyj/pdb
pdb_00001pyj
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
x-ray
1
1.0
3441.336
5'-D(*CP*CP*AP*TP*AP*TP*GP*GP*CP*CP*C)-3'
1
syn
polymer
3414.234
5'-D*GP*GP*GP*CP*CP*AP*TP*AP*TP*GP*G)-3'
1
syn
polymer
no
yes
(DC)(DC)(DA)(DT)(DA)(DT)(XPB)(DG)(DC)(DC)(DC)
CCATATXGCCC
A
polydeoxyribonucleotide
no
no
(DG)(DG)(DG)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG)
GGGCCATATGG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
chem_comp_atom
chem_comp_bond
database_2
pdbx_nmr_software
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Non-polymer description
Data collection
Database references
Derived calculations
1
0
2004-04-20
1
1
2008-04-29
1
2
2011-07-13
1
3
2014-08-06
1
4
2024-05-01
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2003-07-09
REL
REL
This structure was determined using standard 2D homonuclear techniques
1
2D NOESY
0.1 M NaCl
7.00
ambient
298
K
The structures are based on a total of 325 restraints (271 DNA-DNA, 22 POB-DNA, 5 POB-POB, 29 H-bonds).
molecular mechanics in torsion angle space
minimized average structure
1 mM [POB]dG-dC 11mer duplex adduct in 600 ul 10 mM sodium phosphate, 0.1 M NaCl, 0.1 mM EDTA, pH7.0
100% D2O and 90% H2O, 10% D2O
Varian
collection
VNMR
6.1C
Acceryls
data analysis
Felix
97
Hingerty and Broyde
structure solution
DUPLEX
Hingerty and Broyde
refinement
DUPLEX
600
Varian
INOVA
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
+G
7
n
7
XPB
7
A
G
8
n
8
DG
8
A
C
9
n
9
DC
9
A
C
10
n
10
DC
10
A
C
11
n
11
DC
11
A
G
12
n
1
DG
12
B
G
13
n
2
DG
13
B
G
14
n
3
DG
14
B
C
15
n
4
DC
15
B
C
16
n
5
DC
16
B
A
17
n
6
DA
17
B
T
18
n
7
DT
18
B
A
19
n
8
DA
19
B
T
20
n
9
DT
20
B
G
21
n
10
DG
21
B
G
22
n
11
DG
22
B
author_defined_assembly
2
dimeric
A
XPB
7
A
XPB
7
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
1
-10.25
1.50
119.60
109.35
A
A
A
OP1
P
OP2
DC
DC
DC
2
2
2
N
1
-10.27
1.50
119.60
109.33
A
A
A
OP1
P
OP2
DA
DA
DA
3
3
3
N
1
-10.26
1.50
119.60
109.34
A
A
A
OP1
P
OP2
DT
DT
DT
4
4
4
N
1
-10.22
1.50
119.60
109.38
A
A
A
OP1
P
OP2
DA
DA
DA
5
5
5
N
1
-10.21
1.50
119.60
109.39
A
A
A
OP1
P
OP2
DT
DT
DT
6
6
6
N
1
-10.29
1.50
119.60
109.31
A
A
A
OP1
P
OP2
DG
DG
DG
8
8
8
N
1
-3.81
0.40
110.80
106.99
A
A
A
C4
C5
N7
DG
DG
DG
8
8
8
N
1
3.69
0.50
104.30
107.99
A
A
A
C5
N7
C8
DG
DG
DG
8
8
8
N
1
-3.09
0.50
113.10
110.01
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-10.24
1.50
119.60
109.36
A
A
A
OP1
P
OP2
DC
DC
DC
9
9
9
N
1
-10.26
1.50
119.60
109.34
A
A
A
OP1
P
OP2
DC
DC
DC
10
10
10
N
1
-10.23
1.50
119.60
109.37
A
A
A
OP1
P
OP2
DC
DC
DC
11
11
11
N
1
-3.77
0.40
110.80
107.03
B
B
B
C4
C5
N7
DG
DG
DG
12
12
12
N
1
3.73
0.50
104.30
108.03
B
B
B
C5
N7
C8
DG
DG
DG
12
12
12
N
1
-3.16
0.50
113.10
109.94
B
B
B
N7
C8
N9
DG
DG
DG
12
12
12
N
1
-10.23
1.50
119.60
109.37
B
B
B
OP1
P
OP2
DG
DG
DG
13
13
13
N
1
-3.81
0.40
110.80
106.99
B
B
B
C4
C5
N7
DG
DG
DG
13
13
13
N
1
3.68
0.50
104.30
107.98
B
B
B
C5
N7
C8
DG
DG
DG
13
13
13
N
1
-3.13
0.50
113.10
109.97
B
B
B
N7
C8
N9
DG
DG
DG
13
13
13
N
1
-10.23
1.50
119.60
109.37
B
B
B
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-3.78
0.40
110.80
107.02
B
B
B
C4
C5
N7
DG
DG
DG
14
14
14
N
1
3.73
0.50
104.30
108.03
B
B
B
C5
N7
C8
DG
DG
DG
14
14
14
N
1
-3.13
0.50
113.10
109.97
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
1
-10.26
1.50
119.60
109.34
B
B
B
OP1
P
OP2
DC
DC
DC
15
15
15
N
1
-10.25
1.50
119.60
109.35
B
B
B
OP1
P
OP2
DC
DC
DC
16
16
16
N
1
-10.26
1.50
119.60
109.34
B
B
B
OP1
P
OP2
DA
DA
DA
17
17
17
N
1
-10.27
1.50
119.60
109.33
B
B
B
OP1
P
OP2
DT
DT
DT
18
18
18
N
1
-10.24
1.50
119.60
109.36
B
B
B
OP1
P
OP2
DA
DA
DA
19
19
19
N
1
-10.26
1.50
119.60
109.34
B
B
B
OP1
P
OP2
DT
DT
DT
20
20
20
N
1
-10.27
1.50
119.60
109.33
B
B
B
OP1
P
OP2
DG
DG
DG
21
21
21
N
1
-3.79
0.40
110.80
107.01
B
B
B
C4
C5
N7
DG
DG
DG
21
21
21
N
1
3.74
0.50
104.30
108.04
B
B
B
C5
N7
C8
DG
DG
DG
21
21
21
N
1
-3.12
0.50
113.10
109.98
B
B
B
N7
C8
N9
DG
DG
DG
21
21
21
N
1
-10.25
1.50
119.60
109.35
B
B
B
OP1
P
OP2
DG
DG
DG
22
22
22
N
1
-3.84
0.40
110.80
106.96
B
B
B
C4
C5
N7
DG
DG
DG
22
22
22
N
1
3.70
0.50
104.30
108.00
B
B
B
C5
N7
C8
DG
DG
DG
22
22
22
N
1
-3.08
0.50
113.10
110.02
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
A
A
C8
N9
DG
DG
8
8
-0.045
0.007
1.374
1.329
N
1
B
B
C8
N9
DG
DG
12
12
-0.043
0.007
1.374
1.331
N
1
B
B
C8
N9
DG
DG
13
13
-0.044
0.007
1.374
1.330
N
1
B
B
C8
N9
DG
DG
14
14
-0.045
0.007
1.374
1.329
N
1
B
B
C8
N9
DG
DG
21
21
-0.043
0.007
1.374
1.331
N
1
B
B
C8
N9
DG
DG
22
22
-0.044
0.007
1.374
1.330
N
minimized average
Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex
1
N
N
2
N
N
covale
1.599
both
A
DT
6
A
O3'
DT
6
1_555
A
XPB
7
A
P
XPB
7
1_555
covale
1.600
both
A
XPB
7
A
O3'
XPB
7
1_555
A
DG
8
A
P
DG
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
22
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
22
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
22
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
21
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
21
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
21
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
20
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
20
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
19
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
19
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
18
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
18
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
17
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
17
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
B
DC
15
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
B
DC
15
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
B
DC
15
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
14
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
14
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
14
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
13
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
13
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
13
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
12
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
12
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
12
B
N2
DG
1
1_555
DNA
DNA Adduct, DNA
1PYJ
PDB
1
1
1PYJ
CCATAT(XPB)GCCC
1PYJ
PDB
2
12
1PYJ
GGGCCATATGG
1
11
1PYJ
1
11
1PYJ
A
1
1
11
12
22
1PYJ
12
22
1PYJ
B
2
1
11
1
P 1