1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
Bohon, J.
De Los Santos, C.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C10 H14 N5 O6 P S
363.287
n
6-THIO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
31
1331
1338
10.1093/nar/gkg203
12582253
Structural effect of the anticancer agent 6-thioguanine on duplex DNA.
2003
10.2210/pdb1kb1/pdb
pdb_00001kb1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1
SINGLE WAVELENGTH
M
1
1.0
3350.252
5'-D(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3'
1
syn
polymer
3374.210
5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3'
1
syn
polymer
no
yes
(DC)(DG)(DT)(DA)(DC)(S6G)(DC)(DA)(DT)(DG)(DC)
CGTACGCATGC
A
polydeoxyribonucleotide
no
no
(DG)(DC)(DA)(DT)(DG)(DC)(DG)(DT)(DA)(DC)(DG)
GCATGCGTACG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-10.090
1
19
A
1
B
11
-2.544
A_DC1:DG11_B
1
-2.093
0.609
0.183
-0.229
-5.982
1
19
A
2
B
10
-1.984
A_DG2:DC10_B
2
-1.481
-0.624
0.137
-0.252
-1.270
1
20
A
3
B
9
-2.453
A_DT3:DA9_B
3
-5.652
-0.211
0.171
-0.129
-0.064
1
20
A
4
B
8
-2.560
A_DA4:DT8_B
4
-9.040
0.247
0.111
-0.106
2.239
1
19
A
5
B
7
-0.731
A_DC5:DG7_B
5
-4.749
0.825
0.063
-0.269
-2.655
1
A
6
B
6
6.068
A_S6G6:DC6_B
6
-3.214
-1.147
0.262
-0.108
-5.032
1
19
A
7
B
5
-0.994
A_DC7:DG5_B
7
1.818
0.732
0.355
-0.266
-1.558
1
20
A
8
B
4
-2.863
A_DA8:DT4_B
8
-8.438
0.212
0.060
-0.086
7.371
1
20
A
9
B
3
-3.013
A_DT9:DA3_B
9
-8.607
-0.351
0.070
-0.096
5.948
1
19
A
10
B
2
-1.175
A_DG10:DC2_B
10
1.228
-0.645
0.274
-0.269
-5.266
1
19
A
11
B
1
-0.769
A_DC11:DG1_B
11
3.870
0.684
0.316
-0.239
2.630
31.837
A
A
1
2
7.928
B
B
11
10
2.766
4.332
0.567
-1.109
AA_DC1DG2:DC10DG11_BB
1
2.501
-4.578
31.451
-2.678
-0.654
3.038
39.349
A
A
2
3
-1.259
B
B
10
9
3.018
-0.847
-0.102
-1.085
AA_DG2DT3:DA9DC10_BB
2
0.566
-0.840
39.336
-1.518
0.214
2.318
35.998
A
A
3
4
18.803
B
B
9
8
2.831
11.430
0.193
-1.229
AA_DT3DA4:DT8DA9_BB
3
1.004
-1.651
34.177
-3.304
-0.197
2.992
40.590
A
A
4
5
1.352
B
B
8
7
3.005
0.938
-0.270
-0.788
AA_DA4DC5:DG7DT8_BB
4
-0.799
1.152
40.572
-1.232
0.308
2.606
32.339
A
A
5
6
11.642
B
B
7
6
2.867
6.443
0.623
-1.028
AA_DC5S6G6:DC6DG7_BB
5
-0.373
0.673
31.705
-2.809
-1.173
3.260
49.925
A
A
6
7
-4.414
B
B
6
5
3.232
-3.722
-0.491
-0.355
AA_S6G6DC7:DG5DC6_BB
6
-1.257
1.491
49.780
-0.152
0.491
2.374
36.265
A
A
7
8
14.554
B
B
5
4
2.721
8.956
-0.295
-0.943
AA_DC7DA8:DT4DG5_BB
7
3.644
-5.922
34.994
-2.510
0.880
2.780
32.430
A
A
8
9
4.451
B
B
4
3
2.849
2.483
-0.086
-0.839
AA_DA8DT9:DA3DT4_BB
8
-0.477
0.856
32.334
-1.879
0.081
2.795
34.899
A
A
9
10
4.401
B
B
3
2
2.929
2.634
0.352
-1.174
AA_DT9DG10:DC2DA3_BB
9
-3.051
5.097
34.673
-2.307
-0.992
3.768
50.904
A
A
10
11
-14.693
B
B
2
1
3.699
-12.514
0.015
-0.737
AA_DG10DC11:DG1DC2_BB
10
-1.284
1.507
49.425
0.157
-0.121
database_2
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
1
0
2001-11-28
1
1
2008-04-27
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
SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE THYMINE
RCSB
Y
RCSB
2001-11-05
REL
REL
THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED BY THE FULL- RELAXATION MATRIX BACK CALCULATION METHOD. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH- TEMPERATURE STEP MAKE UP THE 15 STRUCTURES. 25 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .59A OR LESS. THE AVERAGE OF THESE 25 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE.
1
2D NOESY
COSY
DQF-COSY
COSY45
TOCSY
HETCO
2D NOESY
25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA
6.78
ambient
298
K
25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA
6.78
ambient
276
K
RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA
100% D2O
2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA
10 % D2O, 90 % H2O
BIOSYM TECHNOLOGIES, INC.
processing
Felix
95 AND 98
BRUNGER
iterative matrix relaxation
X-PLOR
3.857
BRUNGER
refinement
X-PLOR
3.857
600
Varian
INOVA
500
Varian
INOVA
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
S6G
6
n
6
S6G
6
A
C
7
n
7
DC
7
A
A
8
n
8
DA
8
A
T
9
n
9
DT
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
1
n
1
DG
1
B
C
2
n
2
DC
2
B
A
3
n
3
DA
3
B
T
4
n
4
DT
4
B
G
5
n
5
DG
5
B
C
6
n
6
DC
6
B
G
7
n
7
DG
7
B
T
8
n
8
DT
8
B
A
9
n
9
DA
9
B
C
10
n
10
DC
10
B
G
11
n
11
DG
11
B
author_defined_assembly
2
dimeric
A
S6G
6
A
S6G
6
DG
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
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.06
0.50
113.10
116.16
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
2.74
0.30
108.30
111.04
B
B
B
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
3.14
0.50
113.10
116.24
B
B
B
N7
C8
N9
DG
DG
DG
1
1
1
N
1
2.41
0.30
108.30
110.71
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
3.03
0.50
113.10
116.13
B
B
B
N7
C8
N9
DG
DG
DG
5
5
5
N
1
3.13
0.50
113.10
116.23
B
B
B
N7
C8
N9
DG
DG
DG
7
7
7
N
1
3.05
0.50
113.10
116.15
B
B
B
N7
C8
N9
DG
DG
DG
11
11
11
N
1
A
A
C4
N4
DC
DC
1
1
0.095
0.009
1.335
1.430
N
1
A
A
C2
N2
DG
DG
2
2
0.081
0.010
1.341
1.422
N
1
A
A
C5
C7
DT
DT
3
3
0.037
0.006
1.496
1.533
N
1
A
A
C6
N6
DA
DA
4
4
0.094
0.008
1.335
1.429
N
1
A
A
C4
N4
DC
DC
5
5
0.094
0.009
1.335
1.429
N
1
A
A
C4
N4
DC
DC
7
7
0.095
0.009
1.335
1.430
N
1
A
A
C6
N6
DA
DA
8
8
0.094
0.008
1.335
1.429
N
1
A
A
C5
C7
DT
DT
9
9
0.037
0.006
1.496
1.533
N
1
A
A
C2
N2
DG
DG
10
10
0.079
0.010
1.341
1.420
N
1
A
A
C4
N4
DC
DC
11
11
0.094
0.009
1.335
1.429
N
1
B
B
C2
N2
DG
DG
1
1
0.079
0.010
1.341
1.420
N
1
B
B
C4
N4
DC
DC
2
2
0.094
0.009
1.335
1.429
N
1
B
B
C6
N6
DA
DA
3
3
0.093
0.008
1.335
1.428
N
1
B
B
C5
C7
DT
DT
4
4
0.037
0.006
1.496
1.533
N
1
B
B
C2
N2
DG
DG
5
5
0.080
0.010
1.341
1.421
N
1
B
B
C4
N4
DC
DC
6
6
0.094
0.009
1.335
1.429
N
1
B
B
C2
N2
DG
DG
7
7
0.083
0.010
1.341
1.424
N
1
B
B
C5
C7
DT
DT
8
8
0.037
0.006
1.496
1.533
N
1
B
B
C6
N6
DA
DA
9
9
0.093
0.008
1.335
1.428
N
1
B
B
C4
N4
DC
DC
10
10
0.096
0.009
1.335
1.431
N
1
B
B
C2
N2
DG
DG
11
11
0.086
0.010
1.341
1.427
N
SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE CYTOSINE
1
N
N
2
N
N
covale
1.619
both
A
DC
5
A
O3'
DC
5
1_555
A
S6G
6
A
P
S6G
6
1_555
covale
1.618
both
A
S6G
6
A
O3'
S6G
6
1_555
A
DC
7
A
P
DC
7
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
11
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
11
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
11
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
10
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
10
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
10
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
DA
9
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
DA
9
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
8
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
8
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
7
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
7
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
7
B
N2
DG
7
1_555
hydrog
S6G-DC PAIR
A
S6G
6
A
N1
S6G
6
1_555
B
DC
6
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
B
DG
5
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
B
DG
5
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
B
DG
5
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
4
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
4
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
3
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
3
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
2
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
2
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
2
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
1
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
1
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
1
B
N2
DG
1
1_555
DNA
THIOGUANINE, 6-THIOGUANINE, TG, 6TG, S6G, THIOPURINE, DOUBLE HELIX, B-FORM DNA, DNA
1KB1
PDB
1
1KB1
1KB1
PDB
2
1KB1
1
11
1KB1
1
11
1KB1
A
1
1
11
1
11
1KB1
1
11
1KB1
B
2
1
11
1
P 1