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/pdb1kbm/pdb
pdb_00001kbm
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
3389.221
5'-D(*GP*CP*AP*TP*GP*TP*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)(DT)(DG)(DT)(DA)(DC)(DG)
GCATGTGTACG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-5.921
1
19
A
1
B
11
-2.849
A_DC1:DG11_B
1
-4.747
0.635
0.116
-0.251
-11.374
1
19
A
2
B
10
-1.562
A_DG2:DC10_B
2
-3.913
-0.619
0.038
-0.239
-11.111
1
20
A
3
B
9
-3.156
A_DT3:DA9_B
3
-4.109
-0.213
0.268
-0.111
-4.195
1
20
A
4
B
8
-5.898
A_DA4:DT8_B
4
-3.933
0.375
0.161
-0.070
9.644
1
19
A
5
B
7
2.092
A_DC5:DG7_B
5
-2.883
1.003
-0.061
-0.256
-10.506
A
6
B
6
15.812
A_S6G6:DT6_B
6
-6.131
-3.379
-0.119
-0.188
1.023
1
19
A
7
B
5
-0.688
A_DC7:DG5_B
7
-6.444
0.761
0.169
-0.274
-8.314
1
20
A
8
B
4
-0.396
A_DA8:DT4_B
8
-5.531
0.015
0.106
-0.127
4.016
1
20
A
9
B
3
-5.615
A_DT9:DA3_B
9
-6.989
-0.401
0.081
-0.051
11.207
1
19
A
10
B
2
-1.560
A_DG10:DC2_B
10
2.653
-0.688
0.448
-0.270
2.406
1
19
A
11
B
1
-0.616
A_DC11:DG1_B
11
2.705
0.691
0.199
-0.263
2.870
33.659
A
A
1
2
7.986
B
B
11
10
2.987
4.602
0.648
-1.073
AA_DC1DG2:DC10DG11_BB
1
3.699
-6.419
33.151
-2.530
-0.575
3.228
41.561
A
A
2
3
-5.354
B
B
10
9
3.162
-3.794
-0.096
-0.934
AA_DG2DT3:DA9DC10_BB
2
1.136
-1.604
41.381
-0.923
0.253
2.579
37.885
A
A
3
4
8.483
B
B
9
8
2.751
5.485
0.139
-1.056
AA_DT3DA4:DT8DA9_BB
3
2.729
-4.221
37.404
-2.203
0.073
2.850
36.223
A
A
4
5
-0.333
B
B
8
7
2.819
-0.207
0.638
-0.718
AA_DA4DC5:DG7DT8_BB
4
1.815
-2.920
36.179
-1.129
-0.804
2.580
33.192
A
A
5
6
22.628
B
B
7
6
2.961
12.615
0.951
-0.555
AA_DC5S6G6:DT6DG7_BB
5
1.376
-2.468
30.734
-2.838
-1.462
3.079
52.772
A
A
6
7
2.022
B
B
6
5
2.944
1.793
-1.279
0.493
AA_S6G6DC7:DG5DT6_BB
6
-6.124
6.904
52.412
0.448
1.073
2.916
41.199
A
A
7
8
9.437
B
B
5
4
3.021
6.612
0.100
-0.458
AA_DC7DA8:DT4DG5_BB
7
1.824
-2.604
40.649
-1.304
0.037
2.753
31.017
A
A
8
9
3.501
B
B
4
3
2.799
1.871
-0.526
-0.737
AA_DA8DT9:DA3DT4_BB
8
-0.149
0.278
30.962
-1.684
0.960
2.431
34.994
A
A
9
10
8.510
B
B
3
2
2.679
5.087
0.482
-0.996
AA_DT9DG10:DC2DA3_BB
9
-4.463
7.467
34.354
-2.261
-1.332
3.673
50.352
A
A
10
11
-12.903
B
B
2
1
3.609
-10.901
0.206
-0.686
AA_DG10DC11:DG1DC2_BB
10
-0.088
0.104
49.233
0.072
-0.249
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 CYTOSINE
RCSB
Y
RCSB
2001-11-06
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. 29 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .52A OR LESS. THE AVERAGE OF THESE 29 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
NOESY
COSY
DQFCOSY
COSY45
TOCSY
HETCO
NOESY
25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA
6.78
AMBIENT
298
K
25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA
6.78
AMBIENT
276
K
RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
2mM DNA, 25mM PHOSPHATE Buffer, 50mM NaCl, 0.5mM EDTA
100% D2O
2mM DNA, 25mM PHOSPHATE Buffer, 50mM NaCl, 0.5mM EDTA
10 % D2O, 90 % H20
BRUNGER
refinement
X-PLOR
3.851
BIOSYM TECHNOLOGIES, INC.
processing
Felix
95 AND 98
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
T
6
n
6
DT
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
3.02
0.50
113.10
116.12
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
3.53
0.30
108.30
111.83
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.03
0.50
113.10
116.13
A
A
A
N7
C8
N9
DG
DG
DG
10
10
10
N
1
2.54
0.30
108.30
110.84
B
B
B
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
3.13
0.50
113.10
116.23
B
B
B
N7
C8
N9
DG
DG
DG
1
1
1
N
1
2.88
0.30
108.30
111.18
B
B
B
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
3.06
0.50
113.10
116.16
B
B
B
N7
C8
N9
DG
DG
DG
5
5
5
N
1
3.38
0.50
113.10
116.48
B
B
B
N7
C8
N9
DG
DG
DG
7
7
7
N
1
-2.41
0.40
106.40
103.99
B
B
B
C8
N9
C4
DG
DG
DG
7
7
7
N
1
3.01
0.50
113.10
116.11
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
0.080
0.010
1.341
1.421
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
0.095
0.009
1.335
1.430
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
0.096
0.008
1.335
1.431
N
1
A
A
C5
C7
DT
DT
9
9
0.038
0.006
1.496
1.534
N
1
A
A
C2
N2
DG
DG
10
10
0.080
0.010
1.341
1.421
N
1
A
A
C4
N4
DC
DC
11
11
0.093
0.009
1.335
1.428
N
1
B
B
C2
N2
DG
DG
1
1
0.081
0.010
1.341
1.422
N
1
B
B
C4
N4
DC
DC
2
2
0.095
0.009
1.335
1.430
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
0.036
0.006
1.496
1.532
N
1
B
B
C2
N2
DG
DG
5
5
0.084
0.010
1.341
1.425
N
1
B
B
C5
C7
DT
DT
6
6
0.039
0.006
1.496
1.535
N
1
B
B
C2
N2
DG
DG
7
7
0.081
0.010
1.341
1.422
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
0.094
0.008
1.335
1.429
N
1
B
B
C4
N4
DC
DC
10
10
0.094
0.009
1.335
1.429
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 THYMINE
1
N
N
2
N
N
covale
1.617
both
A
DC
5
A
O3'
DC
5
1_555
A
S6G
6
A
P
S6G
6
1_555
covale
1.619
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-DT MISPAIR
A
S6G
6
A
N1
S6G
6
1_555
B
DT
6
B
O2
DT
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
1KBM
PDB
1
1KBM
1KBM
PDB
2
1KBM
1
11
1KBM
1
11
1KBM
A
1
1
11
1
11
1KBM
1
11
1KBM
B
2
1
11
1
P 1