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
C9 H15 N3 O7 P 1
308.205
n
2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C13 H18 N5 O7 P
387.285
n
2'-DEOXY-N1,N2-PROPANO GUANOSINE 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/pdb1laq/pdb
pdb_00001laq
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
4024.636
5'-D(*CP*GP*CP*GP*GP*TP*(P)P*TP*CP*CP*GP*CP*G)-3'
1
syn
polymer
3963.584
5'-D(*CP*GP*CP*GP*GP*AP*(DNR)P*AP*CP*CP*GP*CP*G)-3'
1
syn
polymer
no
yes
(DC)(DG)(DC)(DG)(DG)(DT)(P)(DT)(DC)(DC)(DG)(DC)(DG)
CGCGGTGTCCGCG
A
polydeoxyribonucleotide
no
yes
(DC)(DG)(DC)(DG)(DG)(DA)(DNR)(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
-30.048
1
19
A
1
B
26
-3.491
A_DC1:DG26_B
1
-1.048
0.100
0.723
-0.031
-13.398
1
19
A
2
B
25
-1.865
A_DG2:DC25_B
2
-4.093
-0.136
0.052
-0.120
2.805
1
19
A
3
B
24
-2.765
A_DC3:DG24_B
3
-3.186
0.144
-0.023
-0.109
12.524
1
19
A
4
B
23
-2.871
A_DG4:DC23_B
4
-2.128
-0.137
0.240
-0.090
20.089
1
19
A
5
B
22
-0.027
A_DG5:DC22_B
5
-4.374
-0.172
0.227
-0.045
22.926
1
20
A
6
B
21
3.193
A_DT6:DA21_B
6
-22.716
0.099
-0.504
-0.160
21.889
A
7
B
20
83.671
A_P7:DNR20_B
7
3.309
1.083
-1.328
-3.654
1.073
1
20
A
8
B
19
3.276
A_DT8:DA19_B
8
-9.660
-0.101
-0.116
-0.139
12.980
1
19
A
9
B
18
1.426
A_DC9:DG18_B
9
-21.400
0.192
-0.390
-0.121
5.087
1
19
A
10
B
17
-1.294
A_DC10:DG17_B
10
-17.385
0.164
0.004
-0.104
6.953
1
19
A
11
B
16
-2.033
A_DG11:DC16_B
11
-6.498
-0.153
0.402
-0.101
12.355
1
19
A
12
B
15
-3.014
A_DC12:DG15_B
12
-2.371
0.140
0.210
-0.121
26.636
1
19
A
13
B
14
-3.938
A_DG13:DC14_B
13
-8.039
-0.008
0.711
-0.088
2.834
38.737
A
A
1
2
-6.076
B
B
26
25
2.876
-4.021
-0.112
0.168
AA_DC1DG2:DC25DG26_BB
1
2.308
-3.488
38.469
0.684
0.417
2.763
36.490
A
A
2
3
-5.316
B
B
25
24
2.846
-3.325
-0.078
0.819
AA_DG2DC3:DG24DC25_BB
2
-0.002
0.004
36.343
1.703
0.125
2.767
35.804
A
A
3
4
11.504
B
B
24
23
2.857
7.029
0.487
-0.256
AA_DC3DG4:DC23DG24_BB
3
0.925
-1.515
35.118
-1.294
-0.677
3.005
37.403
A
A
4
5
-0.342
B
B
23
22
2.998
-0.219
0.307
0.120
AA_DG4DG5:DC22DC23_BB
4
1.053
-1.643
37.388
0.213
-0.351
3.040
39.803
A
A
5
6
-6.931
B
B
22
21
3.085
-4.667
0.484
0.479
AA_DG5DT6:DA21DC22_BB
5
9.375
-13.921
38.455
1.220
0.325
0.501
-174.226
A
A
6
7
-2.825
B
B
21
20
-1.351
5.587
-2.825
3.907
AA_DT6P7:DNR20DA21_BB
6
170.145
86.016
-107.421
-1.951
-1.553
-0.378
-175.122
A
A
7
8
-53.710
B
B
20
19
0.332
106.369
1.216
3.208
AA_P7DT8:DA19DNR20_BB
7
-135.366
-68.351
-103.028
-1.601
0.615
2.787
38.398
A
A
8
9
-2.999
B
B
19
18
2.832
-1.971
-0.344
0.625
AA_DT8DC9:DG18DA19_BB
8
1.110
-1.688
38.333
1.161
0.642
3.515
38.616
A
A
9
10
3.519
B
B
18
17
3.480
2.325
-0.578
0.317
AA_DC9DC10:DG17DG18_BB
9
-1.826
2.763
38.507
0.172
0.633
3.229
38.611
A
A
10
11
4.939
B
B
17
16
3.221
3.261
0.271
0.379
AA_DC10DG11:DC16DG17_BB
10
-1.535
2.325
38.449
0.176
-0.597
3.020
39.358
A
A
11
12
-13.697
B
B
16
15
3.226
-9.147
-0.166
0.566
AA_DG11DC12:DG15DC16_BB
11
-0.796
1.192
38.314
1.891
0.155
2.836
39.651
A
A
12
13
-3.075
B
B
15
14
2.853
-2.085
0.335
0.419
AA_DC12DG13:DC14DG15_BB
12
1.042
-1.537
39.585
0.829
-0.387
database_2
entity_poly
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Polymer sequence
1
0
2002-04-17
1
1
2008-04-28
1
2
2011-07-13
2
0
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
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 position.
1lai is the Solution structure of the B-DNA duplex CGCGGTGTCCGCG
1LAS IS THE Solution structure of the B-DNA duplex CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanodeoxyguanosine adduct with the deoxyribose at C20 opposite PdG in the C3' endo conformation.
RCSB
Y
RCSB
2002-03-29
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
5.2
ambient
303
K
100 mM NaCl
5.2
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
P
7
n
7
P
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
DNR
20
n
7
DNR
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
A
P
7
A
P
7
DG
B
DNR
20
B
DNR
7
DC
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
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.50
0.30
108.30
110.80
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.64
0.50
113.10
117.74
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
2.98
0.30
108.30
111.28
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.61
0.40
106.40
103.79
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
3.33
0.30
108.30
111.63
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.03
0.30
108.30
111.33
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.68
0.50
113.10
117.78
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
DG
DG
DG
13
13
13
N
1
-2.94
0.40
106.40
103.46
A
A
A
C8
N9
C4
DG
DG
DG
13
13
13
N
1
2.96
0.30
108.30
111.26
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
2.34
0.30
108.30
110.64
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.65
0.50
113.10
117.75
B
B
B
N7
C8
N9
DG
DG
DG
15
15
15
N
1
-2.54
0.40
106.40
103.86
B
B
B
C8
N9
C4
DG
DG
DG
15
15
15
N
1
3.10
0.30
108.30
111.40
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
2.18
0.30
108.30
110.48
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
4.65
0.50
113.10
117.75
B
B
B
N7
C8
N9
DG
DG
DG
17
17
17
N
1
-2.63
0.40
106.40
103.77
B
B
B
C8
N9
C4
DG
DG
DG
17
17
17
N
1
2.73
0.30
108.30
111.03
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.48
0.50
113.10
117.58
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.63
0.40
106.40
103.77
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.95
0.30
108.30
111.25
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
3.67
0.50
113.80
117.47
B
B
B
N7
C8
N9
DA
DA
DA
19
19
19
N
1
2.88
0.30
108.30
111.18
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
3.40
0.30
108.30
111.70
B
B
B
O4'
C1'
N1
DC
DC
DC
22
22
22
N
1
3.03
0.30
108.30
111.33
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
2.40
0.30
108.30
110.70
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
4.66
0.50
113.10
117.76
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
1
-2.41
0.40
106.40
103.99
B
B
B
C8
N9
C4
DG
DG
DG
24
24
24
N
1
3.17
0.30
108.30
111.47
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
2.73
0.30
108.30
111.03
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
1
4.53
0.50
113.10
117.63
B
B
B
N7
C8
N9
DG
DG
DG
26
26
26
N
1
-2.82
0.40
106.40
103.58
B
B
B
C8
N9
C4
DG
DG
DG
26
26
26
N
minimized average
Solution Structure of the B-DNA Duplex CGCGGTXTCCGCG (X=PdG) Containing the 1,N2-propanodeoxyguanosine Adduct with the Deoxyribose at C20 Opposite PdG in the C2' Endo Conformation.
1
N
N
2
N
N
covale
1.615
both
A
DT
6
A
O3'
DT
6
1_555
A
P
7
A
P
P
7
1_555
covale
1.613
both
A
P
7
A
O3'
P
7
1_555
A
DT
8
A
P
DT
8
1_555
covale
1.617
both
B
DA
19
B
O3'
DA
6
1_555
B
DNR
20
B
P
DNR
7
1_555
covale
1.614
both
B
DNR
20
B
O3'
DNR
7
1_555
B
DA
21
B
P
DA
8
1_555
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
P-DNR PAIR
A
P
7
A
O6
P
7
1_555
B
DNR
20
B
N4
DNR
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
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, propanodeoxyguanosine
1LAQ
PDB
1
1LAQ
1LAQ
PDB
2
1LAQ
1
13
1LAQ
1
13
1LAQ
A
1
1
13
14
26
1LAQ
14
26
1LAQ
B
2
1
13