0.023095
0.000000
0.000000
0.000000
0.023095
0.000000
0.000000
0.000000
0.040783
0.00000
0.00000
0.00000
Heinemann, U.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
43.300
43.300
24.520
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
C11 H16 N5 O6 P
345.248
n
3'-METHYL-2',3'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
N
Y
57
N
C
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
S
C
N
79
N
O
N
80
S
C
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
C
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
H
N
113
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
doub
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
19
427
433
10.1093/nar/19.3.427
2011517
Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix.
1991
Adenine Press, Albany, NY
Structure and Methods. DNA and RNA
0810
0-940030-31-4
3
39
53
Structural Features of G/C-Rich DNA Going A or B
1990
US
Nucleosides and Nucleotides
NUNUD5
0653
0732-8311
9
349
354
X-Ray Studies of DNA Aiming at Elucidating the Sequence-Structure Code
1990
US
Nucleosides and Nucleotides
NUNUD5
0653
0732-8311
7
699
702
X-Ray Crystallographic Studies of the A-Form of DNA
1988
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
15
9531
9550
Crystal Structure Analysis of an A-DNA Fragment at 1.8 Angstroms Resolution: d(GCCCGGGC)
1987
10.2210/pdb1d26/pdb
pdb_00001d26
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
OSCILLATION CAMERA
ARNDT-WONACOTT
x-ray
1
1.0
X31
EMBL/DESY, HAMBURG
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X31
2426.620
DNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3')
1
man
polymer
18.015
water
29
nat
water
no
yes
(DG)(DC)(DC)(DC)(G31)(DG)(DG)(DC)
GCCCGGGC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
2.37
48.06
MICRODIALYSIS
7.00
pH 7.00, MICRODIALYSIS, temperature 277.00K
277.00
WATER
1
MPD
1
BIS-TRIS-PROPANE_HCL
1
MG ACETATE
1
WATER
2
MPD
2
0.881
1
19
A
1
A
8
-3.866
A_DG1:DC8_A
1
-6.088
-0.271
0.195
-0.193
10.328
1
19
A
2
A
7
1.787
A_DC2:DG7_A
2
-12.927
0.265
-0.072
-0.117
9.054
1
19
A
3
A
6
0.649
A_DC3:DG6_A
3
-11.604
0.193
-0.259
-0.195
-3.216
1
19
A
4
A
5
0.256
A_DC4:G315_A
4
-3.896
0.138
0.129
-0.060
3.216
1
19
A
5
A
4
0.256
A_G315:DC4_A
5
-3.896
-0.138
0.129
-0.060
-9.054
1
19
A
6
A
3
0.649
A_DG6:DC3_A
6
-11.604
-0.193
-0.259
-0.195
-10.328
1
19
A
7
A
2
1.787
A_DG7:DC2_A
7
-12.927
-0.265
-0.072
-0.117
-0.881
1
19
A
8
A
1
-3.866
A_DC8:DG1_A
8
-6.088
0.271
0.195
-0.193
2.796
32.905
A
A
1
2
12.333
A
A
8
7
3.074
6.933
0.596
-1.163
AA_DG1DC2:DG7DC8_AA
1
1.732
-3.080
32.140
-3.128
-0.783
2.912
31.496
A
A
2
3
13.599
A
A
7
6
3.399
7.315
-0.152
-1.708
AA_DC2DC3:DG6DG7_AA
2
1.519
-2.824
30.619
-4.483
0.558
3.403
37.133
A
A
3
4
8.138
A
A
6
5
3.667
5.166
0.174
-1.659
AA_DC3DC4:G315DG6_AA
3
-1.315
2.072
36.762
-3.355
-0.464
2.969
22.719
A
A
4
5
7.309
A
A
5
4
3.236
2.872
0.000
-1.938
AA_DC4G315:DC4G315_AA
4
0.000
0.000
22.539
-5.906
0.000
3.403
37.133
A
A
5
6
8.138
A
A
4
3
3.667
5.166
-0.174
-1.659
AA_G315DG6:DC3DC4_AA
5
1.315
-2.072
36.762
-3.355
0.464
2.912
31.496
A
A
6
7
13.600
A
A
3
2
3.399
7.315
0.152
-1.708
AA_DG6DG7:DC2DC3_AA
6
-1.519
2.824
30.619
-4.483
-0.558
2.796
32.905
A
A
7
8
12.332
A
A
2
1
3.074
6.933
-0.596
-1.163
AA_DG7DC8:DG1DC2_AA
7
-1.732
3.080
32.140
-3.128
0.783
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1992-04-07
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
BNL
Y
NDB
1990-09-17
REL
REL
HOH
water
HOH
9
2
HOH
HOH
9
A
HOH
10
2
HOH
HOH
10
A
HOH
11
2
HOH
HOH
11
A
HOH
12
2
HOH
HOH
12
A
HOH
13
2
HOH
HOH
13
A
HOH
14
2
HOH
HOH
14
A
HOH
15
2
HOH
HOH
15
A
HOH
16
2
HOH
HOH
16
A
HOH
17
2
HOH
HOH
17
A
HOH
18
2
HOH
HOH
18
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
21
2
HOH
HOH
21
A
HOH
22
2
HOH
HOH
22
A
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
29
2
HOH
HOH
29
A
HOH
30
2
HOH
HOH
30
A
HOH
31
2
HOH
HOH
31
A
HOH
32
2
HOH
HOH
32
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
37
2
HOH
HOH
37
A
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
C
3
n
3
DC
3
A
C
4
n
4
DC
4
A
+G
5
n
5
G31
5
A
G
6
n
6
DG
6
A
G
7
n
7
DG
7
A
C
8
n
8
DC
8
A
author_defined_assembly
2
dimeric
A
G31
5
A
G31
5
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_556
y,x,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
24.5200000000
1
-4.89
0.80
109.40
104.51
A
A
A
O5'
C5'
C4'
DG
DG
DG
1
1
1
N
1
-20.48
1.50
119.60
99.12
A
A
A
OP1
P
OP2
DC
DC
DC
2
2
2
N
1
26.50
1.20
110.70
137.20
A
A
A
O5'
P
OP1
DC
DC
DC
2
2
2
N
1
-2.79
0.40
121.90
119.11
A
A
A
N3
C4
C5
DC
DC
DC
2
2
2
N
1
10.63
1.20
119.70
130.33
A
A
A
C3'
O3'
P
DC
DC
DC
2
2
3
Y
1
-13.73
1.50
119.60
105.87
A
A
A
OP1
P
OP2
DC
DC
DC
3
3
3
N
1
19.49
1.20
110.70
130.19
A
A
A
O5'
P
OP1
DC
DC
DC
3
3
3
N
1
-9.11
0.80
109.40
100.29
A
A
A
O5'
C5'
C4'
DC
DC
DC
3
3
3
N
1
4.07
0.30
108.30
112.37
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
8.53
1.20
119.70
128.23
A
A
A
C3'
O3'
P
DC
DC
DC
3
3
4
Y
1
16.56
1.90
104.00
120.56
A
A
A
O3'
P
O5'
DC
DC
DC
3
4
4
Y
1
3.07
0.30
108.30
111.37
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
-6.71
0.80
109.40
102.69
A
A
A
O5'
C5'
C4'
DG
DG
DG
6
6
6
N
1
7.64
1.10
109.80
117.44
A
A
A
C5'
C4'
O4'
DG
DG
DG
6
6
6
N
1
3.62
0.50
106.80
110.42
A
A
A
O4'
C1'
C2'
DG
DG
DG
6
6
6
N
1
-5.54
0.60
119.90
114.36
A
A
A
N1
C6
O6
DG
DG
DG
6
6
6
N
1
3.99
0.60
128.60
132.59
A
A
A
C5
C6
O6
DG
DG
DG
6
6
6
N
1
7.24
1.20
119.70
126.94
A
A
A
C3'
O3'
P
DG
DG
DG
6
6
7
Y
1
4.79
0.50
111.90
116.69
A
A
A
C2
N3
C4
DG
DG
DG
7
7
7
N
1
-3.07
0.50
128.60
125.53
A
A
A
N3
C4
C5
DG
DG
DG
7
7
7
N
1
3.08
0.50
111.50
114.58
A
A
A
C5
C6
N1
DG
DG
DG
7
7
7
N
1
-2.41
0.40
110.80
108.39
A
A
A
C4
C5
N7
DG
DG
DG
7
7
7
N
1
8.18
0.90
116.20
124.38
A
A
A
N1
C2
N2
DG
DG
DG
7
7
7
N
1
-6.18
0.70
119.90
113.72
A
A
A
N3
C2
N2
DG
DG
DG
7
7
7
N
1
3.77
0.50
106.80
110.57
A
A
A
O4'
C1'
C2'
DC
DC
DC
8
8
8
N
1
A
A
P
OP1
DG
DG
6
6
-0.116
0.017
1.485
1.369
N
0.16
2.120
6.000
1197
1
3.000
TR
isotropic
TR
isotropic
2.120
6.000
29
190
1
160
0
3.130
5.000
3.920
6.500
4.810
7.500
4.370
7.500
0.015
0.025
0.035
0.050
0.055
0.050
0.074
0.075
0.020
0.030
0.072
0.100
0.132
0.250
0.208
0.250
fix
fix
2.120
6.000
1D26
1303
1.000
1
refinement
NUCLSQ
EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX
1
N
N
2
N
N
covale
1.633
both
A
DC
4
A
O3'
DC
4
1_555
A
G31
5
A
P
G31
5
1_555
covale
1.826
one
A
G31
5
A
C3M
G31
5
1_555
A
DG
6
A
P
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
8
A
N3
DC
8
7_556
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
8
A
O2
DC
8
7_556
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
7_556
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
7
A
N1
DG
7
7_556
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
7
A
O6
DG
7
7_556
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
7
A
N2
DG
7
7_556
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
A
DG
6
A
N1
DG
6
7_556
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
A
DG
6
A
O6
DG
6
7_556
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
A
DG
6
A
N2
DG
6
7_556
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
A
G31
5
A
N1
G31
5
7_556
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
A
G31
5
A
O6
G31
5
7_556
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
A
G31
5
A
N2
G31
5
7_556
hydrog
WATSON-CRICK
A
G31
5
A
N1
G31
5
1_555
A
DC
4
A
N3
DC
4
7_556
hydrog
WATSON-CRICK
A
G31
5
A
N2
G31
5
1_555
A
DC
4
A
O2
DC
4
7_556
hydrog
WATSON-CRICK
A
G31
5
A
O6
G31
5
1_555
A
DC
4
A
N4
DC
4
7_556
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
3
A
N3
DC
3
7_556
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
3
A
O2
DC
3
7_556
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
3
A
N4
DC
3
7_556
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
A
DC
2
A
N3
DC
2
7_556
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
A
DC
2
A
O2
DC
2
7_556
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
A
DC
2
A
N4
DC
2
7_556
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
A
DG
1
A
N1
DG
1
7_556
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
7_556
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
A
DG
1
A
N2
DG
1
7_556
DNA
A-DNA, DOUBLE HELIX, MODIFIED, DNA
1D26
PDB
1
1D26
1
8
1D26
1
8
1D26
A
1
1
8
96
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