1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Weisenseel, J.P.
Reddy, G.R.
Marnett, L.J.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
US
Chem.Res.Toxicol.
CRTOEC
2140
0893-228X
15
127
139
10.1021/tx0101090
11849038
Structure of an oligodeoxynucleotide containing a 1,N(2)-propanodeoxyguanosine adduct positioned in a palindrome derived from the Salmonella typhimurium hisD3052 gene: Hoogsteen pairing at pH 5.2.
2002
10.2210/pdb1lai/pdb
pdb_00001lai
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
3984.572
5'-D(*CP*GP*CP*GP*GP*TP*GP*TP*CP*CP*GP*CP*G)-3'
1
syn
polymer
3962.576
5'-D(*CP*GP*CP*GP*GP*AP*CP*AP*CP*CP*GP*CP*G)-3'
1
syn
polymer
no
no
(DC)(DG)(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DC)(DG)(DC)(DG)
CGCGGTGTCCGCG
A
polydeoxyribonucleotide
no
no
(DC)(DG)(DC)(DG)(DG)(DA)(DC)(DA)(DC)(DC)(DG)(DC)(DG)
CGCGGACACCGCG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-18.025
1
19
A
1
B
26
-3.843
A_DC1:DG26_B
1
-6.776
0.077
0.636
-0.120
-10.488
1
19
A
2
B
25
-1.630
A_DG2:DC25_B
2
-8.001
-0.177
-0.005
-0.078
-1.920
1
19
A
3
B
24
-2.239
A_DC3:DG24_B
3
-4.168
0.125
0.197
-0.132
9.750
1
19
A
4
B
23
-4.046
A_DG4:DC23_B
4
-10.318
-0.057
0.479
-0.148
1.534
1
19
A
5
B
22
-2.206
A_DG5:DC22_B
5
-9.851
-0.169
0.245
-0.084
-3.220
1
20
A
6
B
21
-4.993
A_DT6:DA21_B
6
-18.249
-0.133
0.438
-0.179
-6.806
1
19
A
7
B
20
-2.032
A_DG7:DC20_B
7
-13.833
-0.171
0.141
-0.090
-8.577
1
20
A
8
B
19
-1.106
A_DT8:DA19_B
8
-10.264
-0.124
0.139
-0.092
-16.628
1
19
A
9
B
18
-2.574
A_DC9:DG18_B
9
-4.385
0.118
0.569
-0.098
-8.519
1
19
A
10
B
17
-3.229
A_DC10:DG17_B
10
-10.283
0.085
0.492
-0.144
0.330
1
19
A
11
B
16
-3.011
A_DG11:DC16_B
11
-5.188
-0.130
0.249
-0.126
8.497
1
19
A
12
B
15
-2.397
A_DC12:DG15_B
12
-8.457
0.161
0.083
-0.091
16.715
1
19
A
13
B
14
-3.739
A_DG13:DC14_B
13
-4.129
-0.110
0.654
-0.120
2.891
40.612
A
A
1
2
4.738
B
B
26
25
2.826
3.269
0.584
0.199
AA_DC1DG2:DC25DG26_BB
1
7.268
-10.535
39.854
-0.035
-0.128
2.930
37.921
A
A
2
3
-2.440
B
B
25
24
2.942
-1.583
-0.174
0.367
AA_DG2DC3:DG24DC25_BB
2
-2.921
4.501
37.780
0.747
-0.069
2.831
37.406
A
A
3
4
3.292
B
B
24
23
2.836
2.110
0.156
-0.058
AA_DC3DG4:DC23DG24_BB
3
0.569
-0.888
37.344
-0.332
-0.179
3.258
39.066
A
A
4
5
5.991
B
B
23
22
3.294
3.998
0.417
-0.361
AA_DG4DG5:DC22DC23_BB
4
1.845
-2.765
38.826
-1.023
-0.400
3.317
35.962
A
A
5
6
-6.860
B
B
22
21
3.267
-4.226
-0.445
-0.548
AA_DG5DT6:DA21DC22_BB
5
-0.882
1.431
35.710
-0.279
0.593
3.193
40.388
A
A
6
7
5.704
B
B
21
20
3.204
3.926
0.470
-0.286
AA_DT6DG7:DC20DA21_BB
6
4.066
-5.908
40.007
-0.848
-0.232
3.267
36.427
A
A
7
8
-2.630
B
B
20
19
3.266
-1.644
0.258
-0.108
AA_DG7DT8:DA19DC20_BB
7
0.025
-0.040
36.391
0.056
-0.410
3.483
43.495
A
A
8
9
7.351
B
B
19
18
3.484
5.431
-0.219
0.138
AA_DT8DC9:DG18DA19_BB
8
-2.842
3.847
43.082
-0.375
0.002
3.012
36.515
A
A
9
10
-3.407
B
B
18
17
3.009
-2.132
-0.587
0.406
AA_DC9DC10:DG17DG18_BB
9
-2.378
3.800
36.380
0.920
0.634
2.835
40.289
A
A
10
11
2.704
B
B
17
16
2.829
1.861
0.217
0.069
AA_DC10DG11:DC16DG17_BB
10
1.471
-2.137
40.222
-0.082
-0.171
2.921
37.603
A
A
11
12
-8.110
B
B
16
15
2.974
-5.210
0.086
0.196
AA_DG11DC12:DG15DC16_BB
11
2.030
-3.160
37.200
0.918
0.106
2.822
41.199
A
A
12
13
1.539
B
B
15
14
2.808
1.079
-0.285
0.126
AA_DC12DG13:DC14DG15_BB
12
-6.182
8.816
40.739
0.078
-0.172
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-04-17
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
1la8 is the Solution structure of the DNA 13-mer hairpin CGCGGTGTCCGCG.
1lae is the Solution structure of the DNA 13-mer hairpin CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanodeoxyguanosine adduct at the seventh positon.
1laq is the Solution structure of the B-DNA duplex CGCGGTXTCCGCG (X=PdG)
containing the 1,N2-propanogeoxyguanosine adduct with the deoxyribose at C20
opposite PdG in the C2' endo conformation.
1LAS IS THE Solution structure of the B-DNA duplex CGCGGTXTCCGCG (X=PdG)
containing the 1,N2-propanogeoxyguanosine adduct with the deoxyribose at C20
opposite PdG in the C3' endo conformation.
RCSB
Y
RCSB
2002-03-28
REL
REL
This Synthetic DNA sequence was derived from the hisD3052 gene of salmonella typhimurium.
sample
This Synthetic DNA sequence was derived from the hisD3052 gene of salmonella typhimurium.
sample
1
2D NOESY
DQF-COSY
31P-1H COSY
2D NOESY
100 mM NaCl
6.8
ambient
303
K
100 mM NaCl
6.8
ambient
278
K
Molecular dynamics using a simulated annealing protocol.
1
minimized average structure
1.8 mM DNA strand, 10 mM sodium phosphate, 100 mM NaCl, 50 uM EDTA
D2O
1.8 mM DNA strand, 1 mM sodium phosphate, 100 mM NaCl, 50 uM EDTA
H2O/D2O
Bruker
collection
UXNMR
3.0
Hare, D.
data analysis
Felix
97.0, 2000
Borgias & James
iterative matrix relaxation
MARDIGRAS
3.2
Brunger, A.
refinement
X-PLOR
3.8
500
Bruker
DRX
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
G
5
n
5
DG
5
A
T
6
n
6
DT
6
A
G
7
n
7
DG
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
C
10
n
10
DC
10
A
G
11
n
11
DG
11
A
C
12
n
12
DC
12
A
G
13
n
13
DG
13
A
C
14
n
1
DC
14
B
G
15
n
2
DG
15
B
C
16
n
3
DC
16
B
G
17
n
4
DG
17
B
G
18
n
5
DG
18
B
A
19
n
6
DA
19
B
C
20
n
7
DC
20
B
A
21
n
8
DA
21
B
C
22
n
9
DC
22
B
C
23
n
10
DC
23
B
G
24
n
11
DG
24
B
C
25
n
12
DC
25
B
G
26
n
13
DG
26
B
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
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.04
0.30
108.30
111.34
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.71
0.50
113.10
117.81
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.78
0.40
106.40
103.62
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.75
0.40
106.40
103.65
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
-4.03
0.60
122.90
118.87
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
3.18
0.30
108.30
111.48
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
1
-2.75
0.40
106.40
103.65
A
A
A
C8
N9
C4
DG
DG
DG
7
7
7
N
1
3.49
0.30
108.30
111.79
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-4.18
0.60
122.90
118.72
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
3.38
0.30
108.30
111.68
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
DG
DG
DG
13
13
13
N
1
-2.74
0.40
106.40
103.66
A
A
A
C8
N9
C4
DG
DG
DG
13
13
13
N
1
3.27
0.30
108.30
111.57
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
2.84
0.30
108.30
111.14
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.49
0.50
113.10
117.59
B
B
B
N7
C8
N9
DG
DG
DG
15
15
15
N
1
-2.66
0.40
106.40
103.74
B
B
B
C8
N9
C4
DG
DG
DG
15
15
15
N
1
2.83
0.30
108.30
111.13
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
2.79
0.30
108.30
111.09
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
4.55
0.50
113.10
117.65
B
B
B
N7
C8
N9
DG
DG
DG
17
17
17
N
1
-2.67
0.40
106.40
103.73
B
B
B
C8
N9
C4
DG
DG
DG
17
17
17
N
1
3.25
0.30
108.30
111.55
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.52
0.50
113.10
117.62
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.73
0.40
106.40
103.67
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.36
0.30
108.30
110.66
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
3.90
0.50
113.80
117.70
B
B
B
N7
C8
N9
DA
DA
DA
19
19
19
N
1
3.22
0.30
108.30
111.52
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
2.16
0.30
108.30
110.46
B
B
B
O4'
C1'
N9
DA
DA
DA
21
21
21
N
1
3.91
0.50
113.80
117.71
B
B
B
N7
C8
N9
DA
DA
DA
21
21
21
N
1
3.22
0.30
108.30
111.52
B
B
B
O4'
C1'
N1
DC
DC
DC
22
22
22
N
1
2.95
0.30
108.30
111.25
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
2.72
0.30
108.30
111.02
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
4.48
0.50
113.10
117.58
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
1
-2.50
0.40
106.40
103.90
B
B
B
C8
N9
C4
DG
DG
DG
24
24
24
N
1
2.62
0.30
108.30
110.92
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
2.54
0.30
108.30
110.84
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
1
4.64
0.50
113.10
117.74
B
B
B
N7
C8
N9
DG
DG
DG
26
26
26
N
1
-2.74
0.40
106.40
103.66
B
B
B
C8
N9
C4
DG
DG
DG
26
26
26
N
minimized average
Solution Structure of the B-DNA Duplex CGCGGTGTCCGCG.
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
26
B
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
26
B
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
26
B
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
25
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
25
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
25
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
24
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
24
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
24
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
23
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
23
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
23
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
22
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
22
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
22
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
21
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
21
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
20
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
20
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
20
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
19
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
19
B
N6
DA
6
1_555
hydrog
DC-DG PAIR
A
DC
9
A
N4
DC
9
1_555
B
DG
17
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
18
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
18
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
18
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
17
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
17
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
17
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
16
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
16
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
16
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N3
DC
12
1_555
B
DG
15
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N4
DC
12
1_555
B
DG
15
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
12
A
O2
DC
12
1_555
B
DG
15
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
13
A
N1
DG
13
1_555
B
DC
14
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
13
A
N2
DG
13
1_555
B
DC
14
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
13
A
O6
DG
13
1_555
B
DC
14
B
N4
DC
1
1_555
DNA
DNA, B-type
1LAI
PDB
1
1LAI
1LAI
PDB
2
1LAI
1
13
1LAI
1
13
1LAI
A
1
1
13
14
26
1LAI
14
26
1LAI
B
2
1
13