1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Thiviyanathan, V.
Vyazovkina, K.V.
Gozansky, E.K.
Bichenchova, E.
Abramova, T.V.
Luxon, B.A.
Lebedev, A.V.
Gorenstein, D.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H16 N3 O6 P
305.224
n
2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE
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
C11 H16 N5 O5 P
329.249
n
2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE
DNA linking
C11 H16 N5 O5 P
329.249
n
2'-DEOXY-ADENOSINE-5'-SP-MONOMETHYLPHOSPHONATE
DNA linking
US
Biochemistry
BICHAW
0033
0006-2960
41
827
838
10.1021/bi011551k
11790104
Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry.
2002
10.2210/pdb1k1h/pdb
pdb_00001k1h
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
2448.613
5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3'
1
syn
polymer
2063.577
5'-D(*CP*(CMR)P*(RMP)P*(RMP)P*(SMP)P*(CMR)P*(RMP))-3'
1
syn
polymer
no
no
(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DC)
TGTTTGGC
A
polydeoxyribonucleotide
no
yes
(DC)(CMR)(RMP)(RMP)(SMP)(CMR)(RMP)
CCAAACA
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
5.591
1
20
A
1
B
15
-3.969
A_DT1:RMP15_B
1
3.044
-0.183
0.149
0.016
21.287
1
19
A
2
B
14
1.784
A_DG2:CMR14_B
2
-6.556
-0.349
0.525
0.045
13.941
1
20
A
3
B
13
-4.124
A_DT3:SMP13_B
3
-19.731
-0.439
-0.197
-0.032
6.252
1
20
A
4
B
12
-2.576
A_DT4:RMP12_B
4
-14.813
-0.160
0.080
0.002
-4.979
1
20
A
5
B
11
1.686
A_DT5:RMP11_B
5
-17.556
0.084
0.246
-0.078
2.454
1
19
A
6
B
10
-2.247
A_DG6:CMR10_B
6
-1.748
0.267
0.307
-0.056
14.552
1
19
A
7
B
9
-1.316
A_DG7:DC9_B
7
-3.928
0.257
0.547
-0.032
3.129
36.119
A
A
1
2
-1.441
B
B
15
14
3.109
-0.893
0.448
-0.493
AA_DT1DG2:CMR14RMP15_BB
1
0.872
-1.406
36.098
-0.675
-0.606
3.503
35.928
A
A
2
3
-3.445
B
B
14
13
3.502
-2.121
-0.441
-1.035
AA_DG2DT3:SMP13CMR14_BB
2
3.268
-5.308
35.723
-1.352
1.215
3.593
31.842
A
A
3
4
-4.892
B
B
13
12
3.569
-2.678
0.736
-1.252
AA_DT3DT4:RMP12SMP13_BB
3
-2.481
4.531
31.637
-1.745
-1.840
3.606
35.728
A
A
4
5
-1.452
B
B
12
11
3.551
-0.890
0.661
-1.230
AA_DT4DT5:RMP11RMP12_BB
4
1.657
-2.702
35.680
-1.864
-0.815
3.024
32.768
A
A
5
6
6.585
B
B
11
10
3.081
3.705
-0.676
-0.656
AA_DT5DG6:CMR10RMP11_BB
5
-1.960
3.484
32.506
-1.760
0.881
3.096
34.418
A
A
6
7
-1.656
B
B
10
9
3.100
-0.980
0.368
-0.469
AA_DG6DG7:DC9CMR10_BB
6
-1.275
2.156
34.382
-0.648
-0.810
database_2
pdbx_nmr_exptl_sample_conditions
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
Experimental preparation
1
0
2002-06-19
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_exptl_sample_conditions.pressure_units
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE / DNA DUPLEX
RCSB
Y
RCSB
2001-09-25
REL
1
2D NOESY
DQF-COSY
100 mM
7.0
1
atm
298
K
No dihedral restraints were used.
molecular dynamics matrix relaxation
DNA, 100 mM NaCl, 10 mM Phosphate, 0.1 mM EDTA
H2O, D2O
Varian
processing
VNMR
5.1
Post, Meadows, and Gorenstein
iterative matrix relaxation
MORASS
2.1
UCSF
refinement
Amber
5.0
750
Varian
UNITYPLUS
600
Varian
UNITYPLUS
400
Varian
UNITYPLUS
DT5
1
n
1
DT
1
A
DG
2
n
2
DG
2
A
DT
3
n
3
DT
3
A
DT
4
n
4
DT
4
A
DT
5
n
5
DT
5
A
DG
6
n
6
DG
6
A
DG
7
n
7
DG
7
A
DC3
8
n
8
DC
8
A
DC5
9
n
1
DC
9
B
CMR
10
n
2
CMR
10
B
AMR
11
n
3
RMP
11
B
AMR
12
n
4
RMP
12
B
AMS
13
n
5
SMP
13
B
CMR
14
n
6
CMR
14
B
AR3
15
n
7
RMP
15
B
author_defined_assembly
2
dimeric
B
CMR
10
B
CMR
2
DC
B
RMP
11
B
RMP
3
DA
B
RMP
12
B
RMP
4
DA
B
SMP
13
B
SMP
5
DA
B
CMR
14
B
CMR
6
DC
B
RMP
15
B
RMP
7
DA
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
A
DG
7
0.057
SIDE CHAIN
1
5.32
0.30
108.30
113.62
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
-3.91
0.60
122.90
118.99
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
1
3.31
0.30
108.30
111.61
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-3.85
0.60
122.90
119.05
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
-4.42
0.60
122.90
118.48
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
3.13
0.30
108.30
111.43
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
2.59
0.30
108.30
110.89
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
HETERODUPLEX OF CHIRALLY PURE METHYLPHOSPHONATE/DNA DUPLEX
1
N
N
2
N
N
covale
1.603
both
B
DC
9
B
O3'
DC
1
1_555
B
CMR
10
B
P
CMR
2
1_555
covale
1.610
both
B
CMR
10
B
O3'
CMR
2
1_555
B
RMP
11
B
P
RMP
3
1_555
covale
1.592
both
B
RMP
11
B
O3'
RMP
3
1_555
B
RMP
12
B
P
RMP
4
1_555
covale
1.594
both
B
RMP
12
B
O3'
RMP
4
1_555
B
SMP
13
B
P
SMP
5
1_555
covale
1.595
both
B
SMP
13
B
O3'
SMP
5
1_555
B
CMR
14
B
P
CMR
6
1_555
covale
1.606
both
B
CMR
14
B
O3'
CMR
6
1_555
B
RMP
15
B
P
RMP
7
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
RMP
15
B
N1
RMP
7
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
RMP
15
B
N6
RMP
7
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
CMR
14
B
N3
CMR
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
CMR
14
B
O2
CMR
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
CMR
14
B
N4
CMR
6
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
SMP
13
B
N1
SMP
5
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
SMP
13
B
N6
SMP
5
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
RMP
12
B
N1
RMP
4
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
RMP
12
B
N6
RMP
4
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
RMP
11
B
N1
RMP
3
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
RMP
11
B
N6
RMP
3
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
CMR
10
B
N3
CMR
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
CMR
10
B
O2
CMR
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
CMR
10
B
N4
CMR
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
9
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
9
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
9
B
N4
DC
1
1_555
DNA
methyl phosphonate, anti sense, DNA
1K1H
PDB
1
1K1H
1K1H
PDB
2
1K1H
1
8
1K1H
1
8
1K1H
A
1
1
8
9
15
1K1H
9
15
1K1H
B
2
1
7