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/pdb1las/pdb
pdb_00001las
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
-28.889
1
19
A
1
B
26
-3.670
A_DC1:DG26_B
1
-2.404
0.082
0.725
-0.044
-14.067
1
19
A
2
B
25
-2.045
A_DG2:DC25_B
2
-6.571
-0.133
0.032
-0.122
1.189
1
19
A
3
B
24
-2.921
A_DC3:DG24_B
3
-4.710
0.138
0.029
-0.113
8.640
1
19
A
4
B
23
-3.313
A_DG4:DC23_B
4
-5.620
-0.111
0.260
-0.114
15.243
1
19
A
5
B
22
-1.886
A_DG5:DC22_B
5
-7.938
-0.133
0.390
-0.070
19.148
1
20
A
6
B
21
-4.034
A_DT6:DA21_B
6
-20.644
0.031
0.080
-0.178
19.962
A
7
B
20
76.981
A_P7:DNR20_B
7
2.310
0.691
-0.915
-3.636
1.971
1
20
A
8
B
19
2.742
A_DT8:DA19_B
8
-16.690
-0.088
-0.064
-0.148
8.836
1
19
A
9
B
18
1.218
A_DC9:DG18_B
9
-22.390
0.170
-0.291
-0.135
2.317
1
19
A
10
B
17
-1.539
A_DC10:DG17_B
10
-16.678
0.151
0.099
-0.109
5.694
1
19
A
11
B
16
-2.375
A_DG11:DC16_B
11
-8.111
-0.130
0.392
-0.111
11.563
1
19
A
12
B
15
-3.143
A_DC12:DG15_B
12
-3.249
0.145
0.171
-0.120
25.913
1
19
A
13
B
14
-3.834
A_DG13:DC14_B
13
-7.524
-0.023
0.688
-0.084
2.862
38.903
A
A
1
2
-3.791
B
B
26
25
2.894
-2.522
-0.150
0.222
AA_DC1DG2:DC25DG26_BB
1
2.181
-3.279
38.765
0.603
0.459
2.785
35.950
A
A
2
3
-5.730
B
B
25
24
2.893
-3.531
-0.066
1.002
AA_DG2DC3:DG24DC25_BB
2
-0.161
0.261
35.781
2.061
0.086
2.932
36.689
A
A
3
4
6.661
B
B
24
23
2.945
4.183
0.545
-0.159
AA_DC3DG4:DC23DG24_BB
3
1.751
-2.789
36.418
-0.768
-0.649
2.974
38.920
A
A
4
5
0.011
B
B
23
22
2.973
0.007
0.121
0.333
AA_DG4DG5:DC22DC23_BB
4
0.367
-0.551
38.919
0.499
-0.141
3.017
40.285
A
A
5
6
-17.400
B
B
22
21
3.219
-11.794
0.420
0.346
AA_DG5DT6:DA21DC22_BB
5
4.823
-7.116
38.297
1.809
-0.076
0.011
-179.715
A
A
6
7
-0.628
B
B
21
20
-0.128
1.255
-3.189
3.988
AA_DT6P7:DNR20DA21_BB
6
173.517
86.762
-174.949
-1.994
-1.596
-1.027
179.248
A
A
7
8
-50.237
B
B
20
19
-1.136
-100.459
-0.531
-3.438
AA_P7DT8:DA19DNR20_BB
7
135.348
-67.684
172.452
-1.740
0.237
2.881
39.781
A
A
8
9
-1.316
B
B
19
18
2.893
-0.895
-0.341
0.586
AA_DT8DC9:DG18DA19_BB
8
-0.194
0.285
39.771
0.952
0.482
3.462
38.369
A
A
9
10
3.411
B
B
18
17
3.429
2.240
-0.454
0.395
AA_DC9DC10:DG17DG18_BB
9
-1.706
2.598
38.269
0.306
0.467
3.200
39.203
A
A
10
11
4.485
B
B
17
16
3.175
3.006
0.211
0.550
AA_DC10DG11:DC16DG17_BB
10
-1.086
1.621
39.078
0.469
-0.441
2.963
39.242
A
A
11
12
-13.949
B
B
16
15
3.191
-9.285
-0.175
0.647
AA_DG11DC12:DG15DC16_BB
11
-0.862
1.294
38.161
2.021
0.162
2.827
39.268
A
A
12
13
-0.784
B
B
15
14
2.825
-0.527
0.368
0.385
AA_DC12DG13:DC14DG15_BB
12
0.875
-1.302
39.255
0.628
-0.457
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
1LAB 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-propnaodeoxyguanosine adduct at the seventh position.
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-propnaodeoxyguanosine adduct with the deoxyribose at C20 opposite PdG in the C2' 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
1.8mM DNA strnad, 10 mM sodium phosphate, 100 mM NaCl, 50 uM EDTA
D2O
1.8mM DNA strnad, 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
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.47
0.30
108.30
110.77
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
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.90
0.30
108.30
111.20
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.07
0.30
108.30
111.37
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.63
0.50
113.10
117.73
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.49
0.40
106.40
103.91
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.77
0.30
108.30
111.07
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
-2.92
0.40
106.40
103.48
A
A
A
C8
N9
C4
DG
DG
DG
13
13
13
N
1
3.00
0.30
108.30
111.30
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
2.36
0.30
108.30
110.66
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.66
0.50
113.10
117.76
B
B
B
N7
C8
N9
DG
DG
DG
15
15
15
N
1
-2.49
0.40
106.40
103.91
B
B
B
C8
N9
C4
DG
DG
DG
15
15
15
N
1
3.09
0.30
108.30
111.39
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
2.14
0.30
108.30
110.44
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
4.62
0.50
113.10
117.72
B
B
B
N7
C8
N9
DG
DG
DG
17
17
17
N
1
-2.62
0.40
106.40
103.78
B
B
B
C8
N9
C4
DG
DG
DG
17
17
17
N
1
2.86
0.30
108.30
111.16
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.53
0.50
113.10
117.63
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.66
0.40
106.40
103.74
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.52
0.30
108.30
110.82
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
3.64
0.50
113.80
117.44
B
B
B
N7
C8
N9
DA
DA
DA
19
19
19
N
1
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N9
DA
DA
DA
21
21
21
N
1
4.06
0.50
113.80
117.86
B
B
B
N7
C8
N9
DA
DA
DA
21
21
21
N
1
3.44
0.30
108.30
111.74
B
B
B
O4'
C1'
N1
DC
DC
DC
22
22
22
N
1
2.88
0.30
108.30
111.18
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
2.36
0.30
108.30
110.66
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
4.64
0.50
113.10
117.74
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
1
-2.44
0.40
106.40
103.96
B
B
B
C8
N9
C4
DG
DG
DG
24
24
24
N
1
3.23
0.30
108.30
111.53
B
B
B
O4'
C1'
N1
DC
DC
DC
25
25
25
N
1
2.71
0.30
108.30
111.01
B
B
B
O4'
C1'
N9
DG
DG
DG
26
26
26
N
1
4.52
0.50
113.10
117.62
B
B
B
N7
C8
N9
DG
DG
DG
26
26
26
N
1
-2.92
0.40
106.40
103.48
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 C3' Endo Conformation.
1
N
N
2
N
N
covale
1.616
both
A
DT
6
A
O3'
DT
6
1_555
A
P
7
A
P
P
7
1_555
covale
1.611
both
A
P
7
A
O3'
P
7
1_555
A
DT
8
A
P
DT
8
1_555
covale
1.612
both
B
DA
19
B
O3'
DA
6
1_555
B
DNR
20
B
P
DNR
7
1_555
covale
1.616
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
1LAS
PDB
1
1LAS
1LAS
PDB
2
1LAS
1
13
1LAS
1
13
1LAS
A
1
1
13
14
26
1LAS
14
26
1LAS
B
2
1
13