1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Giri, I.
Johnston, D.S.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C17 H14 O7
330.289
8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1
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
41
5462
5472
10.1021/bi012116t
11969407
MISPAIRING OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT WITH DEOXYADENOSINE RESULTS IN EXTRUSION OF THE MISMATCHED DA TOWARD THE MAJOR GROOVE
2002
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
3003.993
5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
1
syn
polymer
3108.065
5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3'
1
syn
polymer
330.289
8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1
1
syn
non-polymer
no
no
(DA)(DC)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DT)
ACATCGATCT
A
polydeoxyribonucleotide
no
no
(DA)(DG)(DA)(DT)(DA)(DG)(DA)(DT)(DG)(DT)
AGATAGATGT
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
23.636
1
20
A
1
B
20
-3.284
A_DA1:DT20_B
1
-15.373
0.302
0.966
-0.135
7.918
1
19
A
2
B
19
-0.412
A_DC2:DG19_B
2
-12.410
0.239
0.126
-0.148
-10.484
1
20
A
3
B
18
-0.790
A_DA3:DT18_B
3
-3.413
0.343
-0.096
-0.063
-3.645
1
20
A
4
B
17
0.480
A_DT4:DA17_B
4
1.184
0.110
-0.069
-0.104
7.279
1
19
A
5
B
16
-1.440
A_DC5:DG16_B
5
1.640
0.069
-0.236
-0.160
1.776
1
20
A
7
B
14
3.513
A_DA7:DT14_B
6
-3.931
0.239
0.333
0.027
2.900
1
20
A
8
B
13
-0.876
A_DT8:DA13_B
7
-5.532
0.021
-0.121
-0.113
-1.107
1
19
A
9
B
12
-3.174
A_DC9:DG12_B
8
-3.330
0.276
-0.127
-0.208
-10.712
1
20
A
10
B
11
8.016
A_DT10:DA11_B
9
-11.834
0.047
-0.151
-0.078
3.835
35.361
A
A
1
2
-3.586
B
B
20
19
3.809
-2.174
0.156
-0.565
AA_DA1DC2:DG19DT20_BB
1
3.108
-5.126
35.164
-0.554
0.280
3.438
40.566
A
A
2
3
10.115
B
B
19
18
3.608
6.981
-0.417
-0.724
AA_DC2DA3:DT18DG19_BB
2
0.101
-0.146
39.986
-1.889
0.614
3.303
31.353
A
A
3
4
-4.911
B
B
18
17
3.276
-2.651
0.176
-0.511
AA_DA3DT4:DA17DT18_BB
3
-0.707
1.311
31.236
-0.442
-0.460
3.066
35.834
A
A
4
5
0.942
B
B
17
16
3.079
0.580
0.206
-0.287
AA_DT4DC5:DG16DA17_BB
4
-1.136
1.846
35.812
-0.544
-0.487
3.346
28.653
A
A
7
8
-9.967
B
B
14
13
3.334
-4.900
-0.542
-0.809
AA_DA7DT8:DA13DT14_BB
5
3.097
-6.300
28.073
-0.492
1.818
3.392
39.033
A
A
8
9
0.760
B
B
13
12
3.404
0.507
-0.067
-0.800
AA_DT8DC9:DG12DA13_BB
6
-2.193
3.284
38.970
-1.260
-0.175
3.384
29.047
A
A
9
10
10.621
B
B
12
11
3.465
5.281
1.115
-0.830
AA_DC9DT10:DA11DG12_BB
7
4.182
-8.412
28.271
-2.888
-1.246
atom_site
chem_comp
entity
entity_poly
entity_poly_seq
ndb_struct_conf_na
ndb_struct_na_base_pair_step
pdbx_entity_nonpoly
pdbx_entity_src_syn
pdbx_nonpoly_scheme
pdbx_poly_seq_scheme
pdbx_struct_assembly
pdbx_struct_mod_residue
pdbx_struct_oper_list
pdbx_validate_rmsd_angle
struct_asym
struct_conn
struct_ref
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Data collection
Database references
Derived calculations
Non-polymer description
Polymer sequence
Source and taxonomy
Structure summary
1
0
2002-10-16
1
1
2008-04-28
1
2
2011-07-13
2
0
2019-01-30
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.group_PDB
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.type_symbol
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.id
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly_seq.mon_id
_ndb_struct_na_base_pair_step.roll
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.pdb_mon_id
_struct_ref.pdbx_align_begin
NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE
RCSB
Y
RCSB
2002-08-28
REL
REL
AFN
8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1
32630
synthetic construct
sample
1
10
32630
synthetic construct
sample
1
10
40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging Final A and Final B, and after energy Minimization. This energy minimized structure was solvated, and explicit counterions were added. In all, 17 Na+ ions were added to neutralize the system using the Leap module in AMBER 6.0. The SHAKE algorithm constrained bonds involving protons to a tolerance of 0.0005 . A 1 fs time step was used. The rMD calculations were run for 1.4 ns, and coordinates were captured every 200 ps. The emergent structure from AMBER is Being reported
Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure.
20
1
2D NOESY
2D TOCSY
DQF-COSY
P-COSY
T1
0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O
7.4
ATM
278
K
For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O, buffer, containing 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.4
7.4
ATM
273
K
There were 329 experimental distance restraints derived from nonexchangeable 1H NOEs by MARDIGRAS. These consisted of 181 intranucleotide restraints, 110 internucleotide restraints, and 38 adduct-DNA restraints
distance geometry : MardiGras;
simulated annealing molecular dynamics : XPLOR;
Average structure Calculation Addition of Solvent, and Counterions : AMBER;
simulated annealing and Molecular Dynamics matrix relaxation : CORMA;
1
80 OD of d(ACATCAFBGATCT)d(AGATAGATGT) solution in NMR Buffer
For observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O. For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O. Most experiments were performed at 5 C. Spectra of exchangeable protons were obtained at 0 C.
Accelyris, Inc., San Diego, CA
processing
FELIX
97, 2000
Bruker
collection
XWINNMR
4.0
Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487
data analysis
MARDIGRAS
3.2
A.T.Brunger
refinement
X-PLOR
3.1
Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) J. Phys. Chem. 40, 10269-10280
structure solution
AMBER
6.0
Keepers, J. W., and James, T. L. (1984) J. Magn. Reson. 57, 404-426.
data analysis
CORMA
4.0
Accelyris, Inc., San Diego, CA
structure solution
INSIGHTII
2000
Frisch, M. J., Trucks, G. W., et al. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA.
processing
GAUSSIAN 98
1998
500
Bruker
DRX
800
Bruker
DRX
600
Bruker
DRX
X
6
3
AFN
AFN
11
A
A
1
n
1
DA
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
C
5
n
5
DC
5
A
X
6
n
6
DG
6
A
A
7
n
7
DA
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
T
10
n
10
DT
10
A
A
11
n
1
DA
11
B
G
12
n
2
DG
12
B
A
13
n
3
DA
13
B
T
14
n
4
DT
14
B
A
15
n
5
DA
15
B
G
16
n
6
DG
16
B
A
17
n
7
DA
17
B
T
18
n
8
DT
18
B
G
19
n
9
DG
19
B
T
20
n
10
DT
20
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
identity operation
0.0000000000
0.0000000000
0.0000000000
1
B
DA
15
0.102
SIDE CHAIN
1
-4.24
0.60
118.60
114.36
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
1
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.01
0.50
117.70
120.71
A
A
A
C5
C6
N1
DA
DA
DA
3
3
3
N
1
-4.44
0.60
118.60
114.16
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
1
-4.56
0.60
122.90
118.34
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
3.32
0.30
108.30
111.62
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-4.20
0.60
118.60
114.40
A
A
A
N1
C6
N6
DA
DA
DA
7
7
7
N
1
-4.88
0.60
122.90
118.02
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
3.88
0.60
118.90
122.78
A
A
A
N1
C2
O2
DC
DC
DC
9
9
9
N
1
-4.49
0.70
121.90
117.41
A
A
A
N3
C2
O2
DC
DC
DC
9
9
9
N
1
3.69
0.30
108.30
111.99
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
-3.99
0.60
122.90
118.91
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
1
-4.37
0.60
118.60
114.23
B
B
B
N1
C6
N6
DA
DA
DA
11
11
11
N
1
2.48
0.30
108.30
110.78
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
3.86
0.30
108.30
112.16
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
-4.61
0.60
122.90
118.29
B
B
B
C6
C5
C7
DT
DT
DT
14
14
14
N
1
3.39
0.30
108.30
111.69
B
B
B
O4'
C1'
N9
DA
DA
DA
15
15
15
N
1
3.15
0.50
117.70
120.85
B
B
B
C5
C6
N1
DA
DA
DA
15
15
15
N
1
-4.17
0.60
118.60
114.43
B
B
B
N1
C6
N6
DA
DA
DA
15
15
15
N
1
2.60
0.30
108.30
110.90
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-3.74
0.60
122.90
119.16
B
B
B
C6
C5
C7
DT
DT
DT
20
20
20
N
5'-D(*AP*CP*AP*TP*CP*(X)P*AP*TP*CP*T)-3'
SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE
1
N
N
2
N
N
3
N
N
covale
1.507
sing
A
DG
6
A
N7
DG
6
1_555
A
AFN
11
C
C8A
AFN
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
20
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
20
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
18
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
16
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
16
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
16
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
14
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
14
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
13
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
13
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
12
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
12
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
12
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
11
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
B
DA
11
B
N6
DA
1
1_555
DNA
AFLATOXIN B1- Guanine Adduct Opposite an Adenine, mimicking GA Transition, DNA
1MK6
PDB
1
1
1MK6
1MK6
PDB
2
1
1MK6
1
10
1MK6
1
10
1MK6
A
1
1
10
11
20
1MK6
11
20
1MK6
B
2
1
10