1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kool, E.T.
Krugh, T.R.
Guckian, K.M.
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
C12 H15 F2 O6 P
324.214
1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-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
C13 H17 N2 O6 P
328.258
1-[2-DEOXYRIBOFURANOSYL]-4-METHYL-BENZOIMIDAZOLE-5'-MONOPHOSPHATE
DNA linking
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
122
6841
6847
-1
Solution Structure of a Nonpolar, Non-Hydrogen-Bonded Base Pair Surrogate in DNA
2000
10.2210/pdb1eek/pdb
pdb_00001eek
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3615.372
5'-D(*CP*GP*CP*AP*TP*(DFT)P*GP*TP*TP*AP*CP*C)-3'
1
syn
polymer
3708.478
5'-D(*GP*GP*TP*AP*AP*CP*(MBZ)P*AP*TP*GP*CP*G)-3'
1
syn
polymer
no
yes
(DC)(DG)(DC)(DA)(DT)(DFT)(DG)(DT)(DT)(DA)(DC)(DC)
CGCATNGTTACC
1
polydeoxyribonucleotide
no
yes
(DG)(DG)(DT)(DA)(DA)(DC)(MBZ)(DA)(DT)(DG)(DC)(DG)
GGTAACNATGCG
2
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
20.698
1
19
1
1
2
12
-0.926
1_DC1:DG12_2
1
-25.110
0.352
-0.165
-0.115
-0.026
1
19
1
2
2
11
-1.656
1_DG2:DC11_2
2
-11.244
-0.591
0.193
-0.265
-5.540
1
19
1
3
2
10
-1.156
1_DC3:DG10_2
3
-12.167
0.479
0.176
-0.198
-5.841
1
20
1
4
2
9
-1.706
1_DA4:DT9_2
4
-5.014
0.235
0.320
-0.082
1.424
1
20
1
5
2
8
-1.895
1_DT5:DA8_2
5
-10.434
-0.397
0.562
-0.146
-5.607
1
19
1
7
2
6
-2.043
1_DG7:DC6_2
6
-4.594
-0.465
-0.329
-0.236
-6.276
1
20
1
8
2
5
-2.336
1_DT8:DA5_2
7
-10.573
-0.244
0.264
-0.089
-2.821
1
20
1
9
2
4
-1.289
1_DT9:DA4_2
8
-15.481
-0.016
-0.011
-0.110
8.408
1
20
1
10
2
3
-2.727
1_DA10:DT3_2
9
-10.135
0.054
0.322
-0.096
12.919
1
19
1
11
2
2
-1.655
1_DC11:DG2_2
10
-14.851
0.299
-0.190
-0.160
-5.458
1
19
1
12
2
1
-1.986
1_DC12:DG1_2
11
-12.276
0.555
0.375
-0.244
2.677
36.487
1
1
1
2
24.915
2
2
12
11
3.345
15.099
-0.149
-0.915
11_DC1DG2:DC11DG12_22
1
-5.456
9.002
32.874
-3.495
-0.496
3.132
43.394
1
1
2
3
4.986
2
2
11
10
3.191
3.682
0.174
-0.630
11_DG2DC3:DG10DC11_22
2
0.830
-1.124
43.238
-1.198
-0.158
2.424
32.609
1
1
3
4
17.284
2
2
10
9
2.925
9.566
-0.319
-1.363
11_DC3DA4:DT9DG10_22
3
-1.369
2.474
31.181
-3.821
0.368
3.033
33.496
1
1
4
5
-2.563
2
2
9
8
2.983
-1.475
-0.401
-0.720
11_DA4DT5:DA8DT9_22
4
-2.614
4.542
33.365
-1.025
0.300
6.845
68.613
1
1
5
7
-0.227
2
2
8
6
6.802
-0.255
0.931
0.515
11_DT5DG7:DC6DA8_22
5
4.842
-4.298
68.462
0.477
-0.450
3.074
31.711
1
1
7
8
8.631
2
2
6
5
3.283
4.678
-0.488
-1.462
11_DG7DT8:DA5DC6_22
6
-5.410
9.981
30.915
-3.523
-0.087
2.845
39.252
1
1
8
9
7.235
2
2
5
4
2.938
4.840
0.280
-0.719
11_DT8DT9:DA4DA5_22
7
4.354
-6.509
38.730
-1.584
0.046
2.027
29.089
1
1
9
10
25.332
2
2
4
3
2.724
12.316
-0.022
-1.056
11_DT9DA10:DT3DA4_22
8
-2.834
5.828
26.254
-4.168
-0.431
2.940
38.999
1
1
10
11
1.330
2
2
3
2
2.974
0.887
-0.375
-0.651
11_DA10DC11:DG2DT3_22
9
1.737
-2.603
38.952
-1.072
0.751
3.318
33.380
1
1
11
12
4.262
2
2
2
1
3.543
2.442
0.863
-1.550
11_DC11DC12:DG1DG2_22
10
-3.473
6.062
33.117
-3.125
-2.109
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2000-02-16
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
solution structure of an F - A pair
RCSB
Y
RCSB
2000-02-01
REL
1
2D NOESY
100 mM
7.4
ambient
15
K
restrained molecular dynamics
3 mM DNA, phosphate buffer, 100% D2O
100% D2O
500
Varian
UNITY
C
1
n
1
DC
1
1
G
2
n
2
DG
2
1
C
3
n
3
DC
3
1
A
4
n
4
DA
4
1
T
5
n
5
DT
5
1
DFT
6
n
6
DFT
6
1
G
7
n
7
DG
7
1
T
8
n
8
DT
8
1
T
9
n
9
DT
9
1
A
10
n
10
DA
10
1
C
11
n
11
DC
11
1
C
12
n
12
DC
12
1
G
1
n
1
DG
1
2
G
2
n
2
DG
2
2
T
3
n
3
DT
3
2
A
4
n
4
DA
4
2
A
5
n
5
DA
5
2
C
6
n
6
DC
6
2
MBZ
7
n
7
MBZ
7
2
A
8
n
8
DA
8
2
T
9
n
9
DT
9
2
G
10
n
10
DG
10
2
C
11
n
11
DC
11
2
G
12
n
12
DG
12
2
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
1
DA
4
0.118
SIDE CHAIN
1
1
DT
5
0.100
SIDE CHAIN
1
2.35
0.30
108.30
110.65
1
1
1
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
1.86
0.30
108.30
110.16
1
1
1
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
2.32
0.30
108.30
110.62
1
1
1
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
5.51
0.30
108.30
113.81
1
1
1
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
19.65
2.50
111.00
130.65
2
2
2
O5'
C5'
C4'
DG
DG
DG
1
1
1
N
1
2.73
0.30
108.30
111.03
2
2
2
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
3.79
0.30
108.30
112.09
2
2
2
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.21
0.30
108.30
111.51
2
2
2
O4'
C1'
N1
DC
DC
DC
6
6
6
N
SOLUTION STRUCTURE OF A NONPOLAR, NON HYDROGEN BONDED BASE PAIR SURROGATE IN DNA.
1
N
N
2
N
N
covale
1.613
both
1
DT
5
A
O3'
DT
5
1_555
1
DFT
6
A
P
DFT
6
1_555
covale
1.624
both
1
DFT
6
A
O3'
DFT
6
1_555
1
DG
7
A
P
DG
7
1_555
covale
1.597
both
2
DC
6
B
O3'
DC
6
1_555
2
MBZ
7
B
P
MBZ
7
1_555
covale
1.613
one
2
MBZ
7
B
O3'
MBZ
7
1_555
2
DA
8
B
P
DA
8
1_555
hydrog
WATSON-CRICK
1
DC
1
A
N3
DC
1
1_555
2
DG
12
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
1
DC
1
A
N4
DC
1
1_555
2
DG
12
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
1
DC
1
A
O2
DC
1
1_555
2
DG
12
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
1
DG
2
A
N1
DG
2
1_555
2
DC
11
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
1
DG
2
A
N2
DG
2
1_555
2
DC
11
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
1
DG
2
A
O6
DG
2
1_555
2
DC
11
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
1
DC
3
A
N3
DC
3
1_555
2
DG
10
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
1
DC
3
A
N4
DC
3
1_555
2
DG
10
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
1
DC
3
A
O2
DC
3
1_555
2
DG
10
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
1
DA
4
A
N1
DA
4
1_555
2
DT
9
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
1
DA
4
A
N6
DA
4
1_555
2
DT
9
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
1
DT
5
A
N3
DT
5
1_555
2
DA
8
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
1
DT
5
A
O4
DT
5
1_555
2
DA
8
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
1
DG
7
A
N1
DG
7
1_555
2
DC
6
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
1
DG
7
A
N2
DG
7
1_555
2
DC
6
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
1
DG
7
A
O6
DG
7
1_555
2
DC
6
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
1
DT
8
A
N3
DT
8
1_555
2
DA
5
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
1
DT
8
A
O4
DT
8
1_555
2
DA
5
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
1
DT
9
A
N3
DT
9
1_555
2
DA
4
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
1
DT
9
A
O4
DT
9
1_555
2
DA
4
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
1
DA
10
A
N1
DA
10
1_555
2
DT
3
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
1
DA
10
A
N6
DA
10
1_555
2
DT
3
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
1
DC
11
A
N3
DC
11
1_555
2
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
1
DC
11
A
N4
DC
11
1_555
2
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
1
DC
11
A
O2
DC
11
1_555
2
DG
2
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
1
DC
12
A
N3
DC
12
1_555
2
DG
1
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
1
DC
12
A
N4
DC
12
1_555
2
DG
1
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
1
DC
12
A
O2
DC
12
1_555
2
DG
1
B
N2
DG
1
1_555
DNA
DNA, Nonpolar, isosteric, DNA base analogs
1EEK
PDB
1
1EEK
1EEK
PDB
2
1EEK
1
12
1EEK
1
12
1EEK
1
1
1
12
1
12
1EEK
1
12
1EEK
2
2
1
12
1
P 1