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
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
140
152
10.1021/tx010107f
11849039
Structure of the 1,N(2)-propanodeoxyguanosine adduct in a three-base DNA hairpin loop derived from a palindrome in the Salmonella typhimurium hisD3052 gene.
2002
10.2210/pdb1la8/pdb
pdb_00001la8
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
no
no
(DC)(DG)(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DC)(DG)(DC)(DG)
CGCGGTGTCCGCG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
-12.949
1
19
A
1
A
13
-0.749
A_DC1:DG13_A
1
-0.104
0.221
0.223
-0.075
5.200
1
19
A
2
A
12
-3.053
A_DG2:DC12_A
2
2.786
-0.153
0.026
-0.123
-2.493
1
19
A
3
A
11
-2.956
A_DC3:DG11_A
3
-1.406
0.156
0.005
-0.108
11.288
1
19
A
4
A
10
2.036
A_DG4:DC10_A
4
-6.035
-0.124
-0.381
-0.123
20.103
1
19
A
5
A
9
-5.055
A_DG5:DC9_A
5
-2.590
-0.192
0.331
-0.085
2.885
37.926
A
A
1
2
-12.810
A
A
13
12
3.088
-8.262
-0.729
0.526
AA_DC1DG2:DC12DG13_AA
1
1.158
-1.795
37.030
1.787
1.258
4.211
36.457
A
A
2
3
7.097
A
A
12
11
4.246
4.429
0.028
-0.033
AA_DG2DC3:DG11DC12_AA
2
1.345
-2.155
36.172
-0.849
0.197
3.343
34.265
A
A
3
4
1.439
A
A
11
10
3.266
0.846
0.784
0.601
AA_DC3DG4:DC10DG11_AA
3
3.632
-6.175
34.068
0.885
-0.753
3.044
41.262
A
A
4
5
5.066
A
A
10
9
2.753
3.538
-1.369
0.872
AA_DG4DG5:DC9DC10_AA
4
-9.197
13.167
40.118
0.895
1.052
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
1lae is the Solution structure of the 13-mer DNA hairpin CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanodeoxyguanosine adduct.
1lai is the Solution structure of the B-DNA duplex CGCGGTGTCCGCG.
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
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, 10 mM Sodium Phosphate, 100 mM NaCl, 50 uM EDTA
D2O
1.8 mM DNA, 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
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
author_defined_assembly
1
monomeric
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
3.67
0.30
108.30
111.97
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.54
0.40
106.40
103.86
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.42
0.50
113.10
117.52
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
5.28
0.50
113.10
118.38
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
4.64
0.30
108.30
112.94
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
5.49
0.30
108.30
113.79
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
1
-2.58
0.40
106.40
103.82
A
A
A
C8
N9
C4
DG
DG
DG
7
7
7
N
1
3.80
0.30
108.30
112.10
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.19
0.30
108.30
111.49
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
3.28
0.30
108.30
111.58
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.55
0.40
106.40
103.85
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
3.53
0.30
108.30
111.83
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
DG
DG
DG
13
13
13
N
1
-2.88
0.40
106.40
103.52
A
A
A
C8
N9
C4
DG
DG
DG
13
13
13
N
minimized average
Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG
1
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
13
A
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
13
A
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
13
A
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
12
A
N3
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
12
A
O2
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
12
A
N4
DC
12
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
A
DG
11
A
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
A
DG
11
A
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
A
DG
11
A
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
10
A
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
10
A
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
10
A
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
A
DC
9
A
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
A
DC
9
A
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
A
DC
9
A
N4
DC
9
1_555
DNA
DNA, Hairpin, three base loop
1LA8
PDB
1
1LA8
1
13
1LA8
1
13
1LA8
A
1
1
13