0.030989
0.000000
0.014961
0.000000
0.039124
0.000000
0.000000
0.000000
0.031992
0.00000
0.00000
0.00000
Lipscomb, L.A.
Peek, M.E.
Morningstar, M.L.
Verghis, S.M.
Miller, E.M.
Rich, A.
Essigmann, J.M.
Williams, L.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
115.77
90.00
32.270
25.560
34.710
C10 H14 N5 O8 P
363.221
n
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
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
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
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
N
N
16
N
C
N
17
N
C
N
18
N
O
N
19
N
N
N
20
N
C
N
21
N
N
N
22
N
N
N
23
N
C
N
24
N
O
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
H
N
38
N
H
N
39
N
O
N
40
N
P
N
41
N
O
N
42
N
O
N
43
N
O
N
44
N
C
N
45
R
C
N
46
N
O
N
47
S
C
N
48
N
O
N
49
N
C
N
50
R
C
Y
51
N
N
Y
52
N
C
Y
53
N
N
Y
54
N
C
Y
55
N
C
N
56
N
N
Y
57
N
N
Y
58
N
C
Y
59
N
N
Y
60
N
C
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
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
O
N
76
N
P
N
77
N
O
N
78
N
O
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
O
N
83
S
C
N
84
N
O
N
85
N
C
N
86
R
C
N
87
N
N
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
C
N
94
N
C
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
H
N
109
N
O
N
110
N
P
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
C
N
115
R
C
N
116
N
O
N
117
S
C
N
118
N
O
N
119
N
C
N
120
R
C
Y
121
N
N
Y
122
N
C
Y
123
N
N
Y
124
N
C
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
N
Y
131
N
C
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
N
144
N
H
N
145
N
H
N
146
N
O
N
147
N
P
N
148
N
O
N
149
N
O
N
150
N
O
N
151
N
C
N
152
R
C
N
153
N
O
N
154
S
C
N
155
N
O
N
156
N
C
N
157
R
C
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
N
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
C
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
H
N
180
N
H
N
181
N
H
N
182
N
O
N
183
N
H
N
184
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
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
doub
N
32
N
doub
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
doub
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
Y
64
N
sing
Y
65
N
sing
Y
66
N
doub
N
67
N
sing
Y
68
N
sing
Y
69
N
sing
Y
70
N
doub
N
71
N
sing
Y
72
N
doub
N
73
N
sing
N
74
N
sing
Y
75
N
sing
Y
76
N
doub
N
77
N
sing
Y
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
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
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
doub
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
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
Y
137
N
sing
Y
138
N
sing
Y
139
N
doub
N
140
N
sing
Y
141
N
sing
N
142
N
sing
Y
143
N
doub
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
doub
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
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
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
92
719
723
10.1073/pnas.92.3.719
7846041
X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine.
1995
10.2210/pdb183d/pdb
pdb_0000183d
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
AREA DETECTOR
SDMS
x-ray
1
1.0
ROTATING ANODE
RIGAKU RU200
3061.992
DNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3')
1
syn
polymer
18.015
water
42
nat
water
no
yes
(DC)(DC)(DA)(8OG)(DC)(DG)(DC)(DT)(DG)(DG)
CCAGCGCTGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
2.11
41.57
VAPOR DIFFUSION, SITTING DROP
7.60
pH 7.60, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
277.00
WATER
1
MPD
1
BIS-TRIS-PROPANE_HCL
1
MGCL2
1
WATER
2
MPD
2
-5.284
1
19
A
1
A
10
-1.087
A_DC1:DG10_A
1
-10.523
0.084
0.280
-0.120
-0.577
1
19
A
2
A
9
-1.708
A_DC2:DG9_A
2
-10.021
0.315
-0.057
-0.184
0.883
1
20
A
3
A
8
1.143
A_DA3:DT8_A
3
-7.569
-0.002
0.209
-0.184
2.461
1
19
A
4
A
7
-3.930
A_8OG4:DC7_A
4
-6.679
-0.014
0.467
-0.125
2.715
1
19
A
5
A
6
-1.614
A_DC5:DG6_A
5
-8.767
-0.009
-0.094
-0.048
-2.715
1
19
A
6
A
5
-1.614
A_DG6:DC5_A
6
-8.767
0.009
-0.094
-0.048
-2.462
1
19
A
7
A
4
-3.930
A_DC7:8OG4_A
7
-6.679
0.014
0.467
-0.125
-0.883
1
20
A
8
A
3
1.143
A_DT8:DA3_A
8
-7.569
0.002
0.209
-0.184
0.577
1
19
A
9
A
2
-1.708
A_DG9:DC2_A
9
-10.021
-0.315
-0.057
-0.184
5.284
1
19
A
10
A
1
-1.087
A_DG10:DC1_A
10
-10.523
-0.084
0.280
-0.120
3.236
30.456
A
A
1
2
12.563
A
A
10
9
3.276
6.526
-0.451
0.653
AA_DC1DC2:DG9DG10_AA
1
4.624
-8.903
29.411
-0.077
1.794
2.831
50.062
A
A
2
3
-8.916
A
A
9
8
3.265
-7.518
0.170
2.806
AA_DC2DA3:DT8DG9_AA
2
-1.613
1.913
49.505
3.825
-0.310
3.241
24.657
A
A
3
4
20.213
A
A
8
7
3.383
8.430
0.551
0.515
AA_DA38OG4:DC7DT8_AA
3
-3.620
8.681
22.911
-1.504
-2.455
3.333
37.399
A
A
4
5
-1.869
A
A
7
6
3.407
-1.195
-0.233
0.369
AA_8OG4DC5:DG6DC7_AA
4
5.129
-8.024
37.040
0.738
1.062
3.515
42.983
A
A
5
6
9.559
A
A
6
5
3.512
6.976
0.000
0.293
AA_DC5DG6:DC5DG6_AA
5
0.000
0.000
42.440
-0.347
0.000
3.333
37.399
A
A
6
7
-1.869
A
A
5
4
3.407
-1.195
0.233
0.369
AA_DG6DC7:8OG4DC5_AA
6
-5.129
8.024
37.040
0.738
-1.062
3.241
24.657
A
A
7
8
20.213
A
A
4
3
3.383
8.430
-0.551
0.515
AA_DC7DT8:DA38OG4_AA
7
3.620
-8.681
22.911
-1.504
2.455
2.831
50.062
A
A
8
9
-8.915
A
A
3
2
3.265
-7.518
-0.170
2.806
AA_DT8DG9:DC2DA3_AA
8
1.613
-1.913
49.505
3.825
0.310
3.236
30.456
A
A
9
10
12.563
A
A
2
1
3.276
6.526
0.451
0.653
AA_DG9DG10:DC1DC2_AA
9
-4.624
8.903
29.411
-0.077
-1.794
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1995-02-27
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_leaving_atom_flag
BNL
Y
NDB
1994-08-01
REL
HOH
water
HOH
11
2
HOH
HOH
11
A
HOH
12
2
HOH
HOH
12
A
HOH
13
2
HOH
HOH
13
A
HOH
14
2
HOH
HOH
14
A
HOH
15
2
HOH
HOH
15
A
HOH
16
2
HOH
HOH
16
A
HOH
17
2
HOH
HOH
17
A
HOH
18
2
HOH
HOH
18
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
21
2
HOH
HOH
21
A
HOH
22
2
HOH
HOH
22
A
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
29
2
HOH
HOH
29
A
HOH
30
2
HOH
HOH
30
A
HOH
31
2
HOH
HOH
31
A
HOH
32
2
HOH
HOH
32
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
37
2
HOH
HOH
37
A
HOH
38
2
HOH
HOH
38
A
HOH
39
2
HOH
HOH
39
A
HOH
40
2
HOH
HOH
40
A
HOH
41
2
HOH
HOH
41
A
HOH
42
2
HOH
HOH
42
A
HOH
43
2
HOH
HOH
43
A
HOH
44
2
HOH
HOH
44
A
HOH
45
2
HOH
HOH
45
A
HOH
46
2
HOH
HOH
46
A
HOH
47
2
HOH
HOH
47
A
HOH
48
2
HOH
HOH
48
A
HOH
49
2
HOH
HOH
49
A
HOH
50
2
HOH
HOH
50
A
HOH
51
2
HOH
HOH
51
A
HOH
52
2
HOH
HOH
52
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
+G
4
n
4
8OG
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
author_defined_assembly
2
dimeric
A
8OG
4
A
8OG
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
C1'
8OG
4
PLANAR
1
A
DA
3
0.065
SIDE CHAIN
1
A
DG
6
0.094
SIDE CHAIN
1
A
DC
7
0.076
SIDE CHAIN
1
4.36
0.30
108.30
112.66
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
-14.35
1.90
104.00
89.65
A
A
A
O3'
P
O5'
8OG
DC
DC
4
5
5
Y
1
9.89
1.60
120.90
130.79
A
A
A
P
O5'
C5'
DC
DC
DC
5
5
5
N
1
4.81
0.60
118.90
123.71
A
A
A
N1
C2
O2
DC
DC
DC
5
5
5
N
1
9.47
1.20
119.70
129.17
A
A
A
C3'
O3'
P
DC
DC
DG
5
5
6
Y
1
6.02
0.30
108.30
114.32
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
4.22
0.30
108.30
112.52
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
4.40
0.60
118.90
123.30
A
A
A
N1
C2
O2
DC
DC
DC
7
7
7
N
1
-3.89
0.60
123.70
119.81
A
A
A
C5
C6
N1
DT
DT
DT
8
8
8
N
1
-4.52
0.60
122.30
117.78
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
1
-4.20
0.60
122.90
118.70
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
A
A
C5'
C4'
DC
DC
1
1
0.043
0.007
1.512
1.555
N
1
A
A
C5'
C4'
DG
DG
6
6
0.050
0.007
1.512
1.562
N
0.234
0.234
1.600
10.000
3290
95.400
1
2.000
1.600
10.000
42
246
1
203
0
0.020
3.60
1.600
183D
12930
3290
2.000
1
refinement
X-PLOR
X-RAY STRUCTURE OF A DNA DECAMER CONTAINING 7, 8-DIHYDRO-8-OXOGUANINE
1
N
N
2
N
N
covale
1.625
both
A
DA
3
A
O3'
DA
3
1_555
A
8OG
4
A
P
8OG
4
1_555
covale
1.572
both
A
8OG
4
A
O3'
8OG
4
1_555
A
DC
5
A
P
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
10
A
N1
DG
10
2_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
10
A
O6
DG
10
2_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
10
A
N2
DG
10
2_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
9
A
N1
DG
9
2_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
9
A
O6
DG
9
2_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
9
A
N2
DG
9
2_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
8
A
N3
DT
8
2_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
8
A
O4
DT
8
2_555
hydrog
WATSON-CRICK
A
8OG
4
A
N1
8OG
4
1_555
A
DC
7
A
N3
DC
7
2_555
hydrog
WATSON-CRICK
A
8OG
4
A
N2
8OG
4
1_555
A
DC
7
A
O2
DC
7
2_555
hydrog
WATSON-CRICK
A
8OG
4
A
O6
8OG
4
1_555
A
DC
7
A
N4
DC
7
2_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
6
A
N1
DG
6
2_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
6
A
O6
DG
6
2_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
6
A
N2
DG
6
2_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
5
A
N3
DC
5
2_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
5
A
O2
DC
5
2_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
5
A
N4
DC
5
2_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
A
8OG
4
A
N1
8OG
4
2_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
A
8OG
4
A
O6
8OG
4
2_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
A
8OG
4
A
N2
8OG
4
2_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
A
DA
3
A
N1
DA
3
2_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
A
DA
3
A
N6
DA
3
2_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
A
DC
2
A
N3
DC
2
2_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
A
DC
2
A
O2
DC
2
2_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
A
DC
2
A
N4
DC
2
2_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
A
DC
1
A
N3
DC
1
2_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
A
DC
1
A
O2
DC
1
2_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
A
DC
1
A
N4
DC
1
2_555
DNA
B-DNA, DOUBLE HELIX, MODIFIED, DNA
183D
PDB
1
183D
1
10
183D
1
10
183D
A
1
1
10
5
C 1 2 1