1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Li, Z.
Tamura, P.J.
Wilkinson, A.S.
Harris, C.M.
Harris, T.M.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C18 H16 O3
280.318
1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL
non-polymer
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
Biochemistry
BICHAW
0033
0006-2960
40
6743
6755
10.1021/bi002785r
11389588
Intercalation of the (1R,2S,3R,4S)-N6-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in the N-ras codon 61 sequence: DNA sequence effects
2001
10.2210/pdb1i7v/pdb
pdb_00001i7v
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3416.263
5'-D(*CP*GP*GP*AP*CP*AP*(BZA)AP*GP*AP*AP*G)-3'
1
syn
polymer
3291.145
5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'
1
syn
polymer
280.318
1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL
1
syn
non-polymer
no
no
(DC)(DG)(DG)(DA)(DC)(DA)(DA)(DG)(DA)(DA)(DG)
CGGACAAGAAG
A
polydeoxyribonucleotide
no
no
(DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG)
CTTCTTGTCCG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-12.141
1
19
A
1
B
22
-1.770
A_DC1:DG22_B
1
-0.330
0.552
0.336
-0.262
8.065
1
19
A
2
B
21
-2.638
A_DG2:DC21_B
2
0.107
-0.420
0.270
-0.260
0.585
1
19
A
3
B
20
-3.377
A_DG3:DC20_B
3
-4.694
-0.455
-0.052
-0.185
1.325
1
20
A
4
B
19
-0.671
A_DA4:DT19_B
4
-3.268
0.362
-0.078
-0.073
5.538
1
19
A
5
B
18
-0.282
A_DC5:DG18_B
5
-1.748
0.828
-0.195
-0.323
41.889
A
6
B
17
-8.055
A_DA6:DT17_B
6
7.133
0.635
0.863
0.744
-39.092
1
20
A
7
B
16
-18.416
A_DA7:DT16_B
7
23.670
-0.032
0.082
0.344
-2.224
1
19
A
8
B
15
0.283
A_DG8:DC15_B
8
4.233
-0.562
0.125
-0.163
10.331
1
20
A
9
B
14
-4.507
A_DA9:DT14_B
9
-8.415
0.369
0.021
-0.047
5.403
1
20
A
10
B
13
-3.112
A_DA10:DT13_B
10
-7.138
0.074
-0.006
-0.103
7.148
1
19
A
11
B
12
-1.471
A_DG11:DC12_B
11
-6.273
-0.529
0.062
-0.273
2.412
30.451
A
A
1
2
5.949
B
B
22
21
2.477
3.116
0.142
-0.560
AA_DC1DG2:DC21DG22_BB
1
2.513
-4.798
30.193
-1.533
0.106
2.685
35.640
A
A
2
3
25.298
B
B
21
20
3.371
15.025
-0.017
-0.940
AA_DG2DG3:DC20DC21_BB
2
1.392
-2.344
32.383
-3.659
0.225
3.240
38.449
A
A
3
4
5.690
B
B
20
19
3.306
3.742
0.398
-0.476
AA_DG3DA4:DT19DC20_BB
3
-0.683
1.039
38.268
-1.189
-0.690
3.315
37.707
A
A
4
5
-5.833
B
B
19
18
3.299
-3.763
-0.185
-0.396
AA_DA4DC5:DG18DT19_BB
4
1.085
-1.681
37.510
-0.118
0.429
2.930
35.558
A
A
5
6
-18.080
B
B
18
17
3.260
-10.875
-0.898
0.557
AA_DC5DA6:DT17DG18_BB
5
0.725
-1.206
33.898
2.452
1.574
2.378
26.145
A
A
7
8
11.592
B
B
16
15
2.609
5.206
1.268
-0.471
AA_DA7DG8:DC15DT16_BB
6
-1.736
3.865
25.573
-2.133
-3.166
2.964
36.773
A
A
8
9
4.831
B
B
15
14
3.015
3.044
-0.507
-0.293
AA_DG8DA9:DT14DC15_BB
7
1.247
-1.980
36.631
-0.843
0.960
3.231
35.916
A
A
9
10
11.904
B
B
14
13
3.402
7.293
-0.056
-0.535
AA_DA9DA10:DT13DT14_BB
8
-0.329
0.536
35.190
-1.935
0.042
3.118
33.293
A
A
10
11
5.100
B
B
13
12
3.175
2.918
0.008
-0.524
AA_DA10DG11:DC12DT13_BB
9
-0.570
0.996
33.164
-1.383
-0.105
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-03-28
1
1
2007-10-16
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-03-10
REL
REL
BZA
1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL
This structure was determined using 2D homonuclear techniques
back calculated data agree with experimental NOESY spectrum
1
1
2D NOESY
2D NOESY
DQF-COSY
TOCSY
0.1 M NaCl
7.0
1
atm
278
K
0.1 M NaCl
7.0
1
atm
288
K
The structure was based on a total of 485 NOE derived distance constraints.
NOE-restrained molecular dynamics/simulated annealing
1.8 mM oligodeoxynucleotide, 10 mM phosphate buffer, 0.05 mM EDTA, 0.1 M NaCl
90% H2O/10% D2O
1.8 mM oligodeoxynucleotide, 10 mM phosphate buffer, 0.05 mM EDTA, 0.1 M NaCl
100% D2O
Bruker
collection
XwinNMR
2.0
A. Brunger
structure solution
X-PLOR
3.851
Biosym Technologies
processing
Felix
97.0
Borgias, B.A., Thomas, P.D., Li, H., Kumar, A., and Tonelli, M.
refinement
CORMA
5.2
Borgias, B.A., Thomas, P.D., Li, H., Kumar, A., and Tonelli, M.
iterative matrix relaxation
MARDIGRAS
3.0
500
Bruker
DMX
750
Bruker
DMX
ABA
7
3
BZA
BZA
12
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
ABA
7
n
7
DA
7
A
G
8
n
8
DG
8
A
A
9
n
9
DA
9
A
A
10
n
10
DA
10
A
G
11
n
11
DG
11
A
C
12
n
1
DC
12
B
T
13
n
2
DT
13
B
T
14
n
3
DT
14
B
C
15
n
4
DC
15
B
T
16
n
5
DT
16
B
T
17
n
6
DT
17
B
G
18
n
7
DG
18
B
T
19
n
8
DT
19
B
C
20
n
9
DC
20
B
C
21
n
10
DC
21
B
G
22
n
11
DG
22
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
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.19
0.30
108.30
111.49
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
3.33
0.30
108.30
111.63
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
2.59
0.30
108.30
110.89
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
3.64
0.50
113.80
117.44
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
-2.49
0.40
105.80
103.31
A
A
A
C8
N9
C4
DA
DA
DA
6
6
6
N
1
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
DA
DA
DA
7
7
7
N
1
3.21
0.30
108.30
111.51
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.80
0.50
113.80
117.60
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
3.03
0.30
108.30
111.33
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
3.06
0.30
108.30
111.36
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
2.80
0.30
108.30
111.10
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.27
0.30
108.30
110.57
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
1.90
0.30
108.30
110.20
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
-4.03
0.60
122.90
118.87
B
B
B
C6
C5
C7
DT
DT
DT
16
16
16
N
1
2.81
0.30
108.30
111.11
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
3.50
0.30
108.30
111.80
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.59
0.50
113.10
117.69
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.71
0.40
106.40
103.69
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.80
0.30
108.30
111.10
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
3.18
0.30
108.30
111.48
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
2.76
0.30
108.30
111.06
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
2.81
0.30
108.30
111.11
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.52
0.50
113.10
117.62
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.64
0.40
106.40
103.76
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
THE SOLUTION STRUCTURE OF A BAY REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE
1
N
N
2
N
N
3
N
N
covale
1.344
none
A
DA
7
A
N6
DA
7
1_555
A
BZA
12
C
C4C
BZA
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
22
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
22
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
22
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
21
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
21
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
21
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
20
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
20
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
20
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
19
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
19
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
18
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
18
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
18
B
N2
DG
7
1_555
hydrog
DA-DT PAIR
A
DA
6
A
N6
DA
6
1_555
B
DT
17
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
16
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
16
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
B
DC
15
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
B
DC
15
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
B
DC
15
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N1
DA
9
1_555
B
DT
14
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N6
DA
9
1_555
B
DT
14
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
B
DT
13
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
B
DT
13
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
12
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
12
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
12
B
N4
DC
1
1_555
DNA
Benz[a]anthracene-DNA duplex, DNA
1I7V
PDB
1
1I7V
1I7V
PDB
2
1I7V
1
11
1I7V
1
11
1I7V
A
1
1
11
12
22
1I7V
12
22
1I7V
B
2
1
11
BINDING SITE FOR RESIDUE BZA A 12
A
BZA
12
Software
6
A
DA
6
A
DA
6
6
1_555
A
DA
7
A
DA
7
6
1_555
A
DG
8
A
DG
8
6
1_555
B
DC
15
B
DC
4
6
1_555
B
DT
16
B
DT
5
6
1_555
B
DT
17
B
DT
6
6
1_555
1
P 1