0.056117
0.000000
0.000000
0.000000
0.032852
0.000000
0.000000
0.000000
0.022462
0.00000
0.00000
0.00000
Zhou, G.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
17.820
30.440
44.520
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H13 N2 O8 P
308.182
y
2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
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
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
Y
50
N
N
Y
51
N
C
Y
52
N
N
Y
53
N
C
Y
54
N
C
N
55
N
N
Y
56
N
N
Y
57
N
C
Y
58
N
N
Y
59
N
C
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
H
N
73
N
H
N
74
N
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
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
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
N
C
N
122
R
C
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
O
N
129
N
C
N
130
N
C
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
MG
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
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
N
59
N
sing
N
60
N
sing
N
61
N
sing
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
sing
Y
67
N
sing
Y
68
N
doub
N
69
N
sing
Y
70
N
doub
N
71
N
sing
N
72
N
sing
Y
73
N
sing
Y
74
N
doub
N
75
N
sing
Y
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
29
7229
7236
10.1021/bi00483a010
2207101
Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG).
1990
10.2210/pdb1d41/pdb
pdb_00001d41
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ROOM TEMPERATURE
1
IMAGE PLATE
RIGAKU
x-ray
1
1.0
1823.245
DNA (5'-D(*(5CM)P*GP*UP*AP*(5CM)P*G)-3')
2
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
60
nat
water
no
yes
(5CM)(DG)(DU)(DA)(5CM)(DG)
CGUACG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1.66
25.71
VAPOR DIFFUSION
7.00
pH 7.00, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
WATER
2
MPD
2
9.603
1
19
A
1
B
12
1.140
A_5CM1:DG12_B
1
0.654
-0.373
-0.057
-0.194
-8.635
1
19
A
2
B
11
3.792
A_DG2:5CM11_B
2
5.542
0.233
0.148
-0.182
6.575
1
20
A
3
B
10
-1.049
A_DU3:DA10_B
3
-7.867
-0.220
0.303
-0.180
-6.124
1
20
A
4
B
9
2.754
A_DA4:DU9_B
4
-3.211
0.142
-0.014
-0.057
-0.009
1
19
A
5
B
8
-0.128
A_5CM5:DG8_B
5
-0.801
-0.350
0.026
-0.173
-3.364
1
19
A
6
B
7
-0.735
A_DG6:5CM7_B
6
-2.506
0.226
0.056
-0.127
3.958
-11.696
A
A
1
2
-0.418
B
B
12
11
4.068
0.085
0.188
5.702
AA_5CM1DG2:5CM11DG12_BB
1
1.678
8.261
-11.575
-28.124
3.752
3.221
-46.924
A
A
2
3
-0.322
B
B
11
10
3.227
0.256
-0.174
-0.627
AA_DG2DU3:DA105CM11_BB
2
-1.901
-2.389
-46.887
0.767
-0.373
6.221
-15.754
A
A
3
4
39.429
B
B
10
9
3.873
-9.946
0.309
5.254
AA_DU3DA4:DU9DA10_BB
3
2.250
8.919
-12.025
-6.039
4.097
3.384
-48.458
A
A
4
5
1.419
B
B
9
8
3.409
-1.165
-0.279
-1.142
AA_DA45CM5:DG8DU9_BB
4
0.258
0.314
-48.444
1.484
-0.320
3.608
-14.290
A
A
5
6
1.192
B
B
8
7
3.558
-0.295
0.000
5.551
AA_5CM5DG6:5CM7DG8_BB
5
-2.702
-10.928
-14.031
-22.017
-2.735
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
1992-04-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
1
4
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1991-05-07
REL
REL
MG
MAGNESIUM ION
HOH
water
1VTW
ZDFB06 IN WHICH THE METHYL GROUPS OF THE THYMINE BASES WERE REMOVED FROM THE C5 POSITIONS.
PDB
experimental model
MO5
13
2
MG
MG
13
B
MO6
14
2
MG
MG
14
B
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
24
3
HOH
HOH
24
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
29
3
HOH
HOH
29
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
44
3
HOH
HOH
44
A
HOH
46
3
HOH
HOH
46
A
HOH
48
3
HOH
HOH
48
A
HOH
49
3
HOH
HOH
49
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
55
3
HOH
HOH
55
A
HOH
58
3
HOH
HOH
58
A
HOH
63
3
HOH
HOH
63
A
MO6
14
3
HOH
HOH
69
A
MO6
14
3
HOH
HOH
71
A
MO6
14
3
HOH
HOH
72
A
MO6
14
3
HOH
HOH
73
A
MO6
14
3
HOH
HOH
74
A
HOH
15
3
HOH
HOH
15
B
HOH
22
3
HOH
HOH
22
B
HOH
23
3
HOH
HOH
23
B
HOH
25
3
HOH
HOH
25
B
HOH
28
3
HOH
HOH
28
B
HOH
30
3
HOH
HOH
30
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
HOH
35
3
HOH
HOH
35
B
HOH
42
3
HOH
HOH
42
B
HOH
43
3
HOH
HOH
43
B
HOH
45
3
HOH
HOH
45
B
HOH
47
3
HOH
HOH
47
B
HOH
50
3
HOH
HOH
50
B
HOH
56
3
HOH
HOH
56
B
HOH
57
3
HOH
HOH
57
B
HOH
59
3
HOH
HOH
59
B
HOH
60
3
HOH
HOH
60
B
HOH
61
3
HOH
HOH
61
B
HOH
62
3
HOH
HOH
62
B
MO5
13
3
HOH
HOH
64
B
MO5
13
3
HOH
HOH
65
B
MO5
13
3
HOH
HOH
66
B
MO5
13
3
HOH
HOH
67
B
MO5
13
3
HOH
HOH
68
B
MO6
14
3
HOH
HOH
70
B
+C
1
n
1
5CM
1
A
G
2
n
2
DG
2
A
U
3
n
3
DU
3
A
A
4
n
4
DA
4
A
+C
5
n
5
5CM
5
A
G
6
n
6
DG
6
A
+C
7
n
1
5CM
7
B
G
8
n
2
DG
8
B
U
9
n
3
DU
9
B
A
10
n
4
DA
10
B
+C
11
n
5
5CM
11
B
G
12
n
6
DG
12
B
author_defined_assembly
2
dimeric
A
HOH
69
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
71
E
O
HOH
1_555
94.3
A
HOH
69
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
72
E
O
HOH
1_555
85.9
A
HOH
71
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
72
E
O
HOH
1_555
177.3
A
HOH
69
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
73
E
O
HOH
1_555
85.9
A
HOH
71
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
73
E
O
HOH
1_555
82.6
A
HOH
72
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
73
E
O
HOH
1_555
94.7
A
HOH
69
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
74
E
O
HOH
1_555
92.3
A
HOH
71
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
74
E
O
HOH
1_555
83.9
A
HOH
72
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
74
E
O
HOH
1_555
98.8
A
HOH
73
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
A
HOH
74
E
O
HOH
1_555
166.2
A
HOH
69
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
B
HOH
70
F
O
HOH
1_555
175.0
A
HOH
71
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
B
HOH
70
F
O
HOH
1_555
89.5
A
HOH
72
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
B
HOH
70
F
O
HOH
1_555
90.2
A
HOH
73
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
B
HOH
70
F
O
HOH
1_555
91.3
A
HOH
74
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
B
HOH
70
F
O
HOH
1_555
91.3
B
DU
9
B
OP2
DU
3
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
64
F
O
HOH
1_555
91.5
B
DU
9
B
OP2
DU
3
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
65
F
O
HOH
1_555
89.0
B
HOH
64
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
65
F
O
HOH
1_555
172.7
B
DU
9
B
OP2
DU
3
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
66
F
O
HOH
1_555
91.3
B
HOH
64
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
66
F
O
HOH
1_555
89.9
B
HOH
65
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
66
F
O
HOH
1_555
82.9
B
DU
9
B
OP2
DU
3
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
67
F
O
HOH
1_555
96.8
B
HOH
64
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
67
F
O
HOH
1_555
105.1
B
HOH
65
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
67
F
O
HOH
1_555
82.0
B
HOH
66
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
67
F
O
HOH
1_555
162.6
B
DU
9
B
OP2
DU
3
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
172.0
B
HOH
64
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
96.0
B
HOH
65
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
83.2
B
HOH
66
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
86.0
B
HOH
67
F
O
HOH
1_555
B
MG
13
C
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
83.9
A
5CM
1
A
5CM
1
DC
A
5CM
5
A
5CM
5
DC
B
5CM
7
B
5CM
1
DC
B
5CM
11
B
5CM
5
DC
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
A
O
O
HOH
HOH
19
39
1.69
1
A
A
O3'
O
DG
HOH
2
20
1.92
1
B
B
C5'
O
5CM
HOH
7
30
2.16
1
17.28
1.50
119.60
136.88
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
-15.22
0.90
105.70
90.48
A
A
A
O5'
P
OP1
DG
DG
DG
2
2
2
N
1
8.58
1.20
110.70
119.28
A
A
A
O5'
P
OP2
DG
DG
DG
2
2
2
N
1
6.14
0.90
103.10
109.24
A
A
A
C4'
C3'
C2'
DG
DG
DG
2
2
2
N
1
6.77
0.60
123.90
130.67
A
A
A
N1
C2
N3
DG
DG
DG
2
2
2
N
1
3.90
0.40
110.80
114.70
A
A
A
C4
C5
N7
DG
DG
DG
2
2
2
N
1
-3.77
0.50
104.30
100.53
A
A
A
C5
N7
C8
DG
DG
DG
2
2
2
N
1
-8.11
0.70
119.90
111.79
A
A
A
N3
C2
N2
DG
DG
DG
2
2
2
N
1
-4.63
0.60
128.60
123.97
A
A
A
C5
C6
O6
DG
DG
DG
2
2
2
N
1
-13.74
2.20
105.20
91.46
A
A
A
O3'
P
OP1
DG
DU
DU
2
3
3
Y
1
-17.52
0.80
109.40
91.88
A
A
A
O5'
C5'
C4'
DU
DU
DU
3
3
3
N
1
-2.78
0.40
104.50
101.72
A
A
A
O4'
C4'
C3'
DU
DU
DU
3
3
3
N
1
7.25
0.90
103.10
110.35
A
A
A
C4'
C3'
C2'
DU
DU
DU
3
3
3
N
1
-10.61
0.80
102.40
91.79
A
A
A
C3'
C2'
C1'
DU
DU
DU
3
3
3
N
1
-5.45
0.70
108.00
102.55
A
A
A
O4'
C1'
N1
DU
DU
DU
3
3
3
N
1
-6.46
0.80
109.40
102.94
A
A
A
O5'
C5'
C4'
DA
DA
DA
4
4
4
N
1
-15.47
2.50
109.70
94.23
A
A
A
C4'
C3'
O3'
DA
DA
DA
4
4
4
N
1
7.40
1.20
102.50
109.90
A
A
A
C3'
C2'
C1'
DA
DA
DA
4
4
4
N
1
-5.13
0.80
105.90
100.77
A
A
A
O4'
C1'
C2'
DA
DA
DA
4
4
4
N
1
-3.42
0.50
103.90
100.48
A
A
A
C5
N7
C8
DA
DA
DA
4
4
4
N
1
-7.56
0.90
105.70
98.14
A
A
A
O5'
P
OP1
DG
DG
DG
6
6
6
N
1
8.55
1.20
110.70
119.25
A
A
A
O5'
P
OP2
DG
DG
DG
6
6
6
N
1
-13.23
0.80
109.40
96.17
A
A
A
O5'
C5'
C4'
DG
DG
DG
6
6
6
N
1
-12.87
1.60
120.90
108.03
A
A
A
P
O5'
C5'
DG
DG
DG
6
6
6
N
1
9.35
0.60
106.00
115.35
A
A
A
O4'
C4'
C3'
DG
DG
DG
6
6
6
N
1
-4.50
0.70
102.20
97.70
A
A
A
C4'
C3'
C2'
DG
DG
DG
6
6
6
N
1
8.48
1.20
102.50
110.98
A
A
A
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
1
-9.07
0.60
125.10
116.03
A
A
A
C6
N1
C2
DG
DG
DG
6
6
6
N
1
6.97
0.60
123.90
130.87
A
A
A
N1
C2
N3
DG
DG
DG
6
6
6
N
1
-5.07
0.50
111.90
106.83
A
A
A
C2
N3
C4
DG
DG
DG
6
6
6
N
1
4.96
0.50
111.50
116.46
A
A
A
C5
C6
N1
DG
DG
DG
6
6
6
N
1
3.42
0.40
106.40
109.82
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
1
-8.82
0.70
119.90
111.08
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
-4.92
0.60
119.90
114.98
A
A
A
N1
C6
O6
DG
DG
DG
6
6
6
N
1
-10.63
0.80
109.40
98.77
B
B
B
O5'
C5'
C4'
DG
DG
DG
8
8
8
N
1
-12.94
1.80
114.10
101.16
B
B
B
C5'
C4'
C3'
DG
DG
DG
8
8
8
N
1
7.34
1.10
109.80
117.14
B
B
B
C5'
C4'
O4'
DG
DG
DG
8
8
8
N
1
7.60
0.50
106.80
114.40
B
B
B
O4'
C1'
C2'
DG
DG
DG
8
8
8
N
1
-7.17
0.60
125.10
117.93
B
B
B
C6
N1
C2
DG
DG
DG
8
8
8
N
1
4.63
0.60
123.90
128.53
B
B
B
N1
C2
N3
DG
DG
DG
8
8
8
N
1
6.21
0.50
111.50
117.71
B
B
B
C5
C6
N1
DG
DG
DG
8
8
8
N
1
4.21
0.40
110.80
115.01
B
B
B
C4
C5
N7
DG
DG
DG
8
8
8
N
1
-3.70
0.40
105.40
101.70
B
B
B
N9
C4
C5
DG
DG
DG
8
8
8
N
1
4.94
0.60
126.00
130.94
B
B
B
N3
C4
N9
DG
DG
DG
8
8
8
N
1
-8.12
0.70
119.90
111.78
B
B
B
N3
C2
N2
DG
DG
DG
8
8
8
N
1
-5.19
0.60
128.60
123.41
B
B
B
C5
C6
O6
DG
DG
DG
8
8
8
N
1
9.97
1.20
119.70
129.67
B
B
B
C3'
O3'
P
DG
DG
DU
8
8
9
Y
1
-14.36
1.50
119.60
105.24
B
B
B
OP1
P
OP2
DU
DU
DU
9
9
9
N
1
7.27
1.20
110.70
117.97
B
B
B
O5'
P
OP1
DU
DU
DU
9
9
9
N
1
-5.04
0.80
109.40
104.36
B
B
B
O5'
C5'
C4'
DU
DU
DU
9
9
9
N
1
-3.38
0.40
104.50
101.12
B
B
B
O4'
C4'
C3'
DU
DU
DU
9
9
9
N
1
8.76
1.20
115.70
124.46
B
B
B
C5'
C4'
C3'
DU
DU
DU
9
9
9
N
1
-8.67
0.80
102.40
93.73
B
B
B
C3'
C2'
C1'
DU
DU
DU
9
9
9
N
1
-5.74
0.70
108.00
102.26
B
B
B
O4'
C1'
N1
DU
DU
DU
9
9
9
N
1
4.84
0.60
121.00
125.84
B
B
B
C6
N1
C2
DU
DU
DU
9
9
9
N
1
-6.44
0.50
122.70
116.26
B
B
B
C5
C6
N1
DU
DU
DU
9
9
9
N
1
-5.18
0.70
119.40
114.22
B
B
B
N3
C4
O4
DU
DU
DU
9
9
9
N
1
8.41
1.20
119.70
128.11
B
B
B
C3'
O3'
P
DU
DU
DA
9
9
10
Y
1
-7.20
0.90
105.70
98.50
B
B
B
O5'
P
OP2
DA
DA
DA
10
10
10
N
1
-5.03
0.80
109.40
104.37
B
B
B
O5'
C5'
C4'
DA
DA
DA
10
10
10
N
1
-3.99
0.40
104.50
100.51
B
B
B
O4'
C4'
C3'
DA
DA
DA
10
10
10
N
1
9.15
0.70
110.30
119.45
B
B
B
C1'
O4'
C4'
DA
DA
DA
10
10
10
N
1
8.32
0.90
103.10
111.42
B
B
B
C4'
C3'
C2'
DA
DA
DA
10
10
10
N
1
-4.85
0.80
105.90
101.05
B
B
B
O4'
C1'
C2'
DA
DA
DA
10
10
10
N
1
6.44
0.30
108.30
114.74
B
B
B
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
-3.68
0.50
129.30
125.62
B
B
B
N1
C2
N3
DA
DA
DA
10
10
10
N
1
-3.14
0.40
105.80
102.66
B
B
B
N9
C4
C5
DA
DA
DA
10
10
10
N
1
4.78
0.60
118.60
123.38
B
B
B
N1
C6
N6
DA
DA
DA
10
10
10
N
1
-5.10
0.80
123.70
118.60
B
B
B
C5
C6
N6
DA
DA
DA
10
10
10
N
1
8.71
1.20
119.70
128.41
B
B
B
C3'
O3'
P
DA
DA
5CM
10
10
11
Y
1
11.38
1.20
110.70
122.08
B
B
B
O5'
P
OP1
DG
DG
DG
12
12
12
N
1
-16.59
0.90
105.70
89.11
B
B
B
O5'
P
OP2
DG
DG
DG
12
12
12
N
1
-9.83
0.40
104.50
94.67
B
B
B
O4'
C4'
C3'
DG
DG
DG
12
12
12
N
1
7.70
1.20
115.70
123.40
B
B
B
C5'
C4'
C3'
DG
DG
DG
12
12
12
N
1
9.54
0.90
103.10
112.64
B
B
B
C4'
C3'
C2'
DG
DG
DG
12
12
12
N
1
-5.60
0.80
102.40
96.80
B
B
B
C3'
C2'
C1'
DG
DG
DG
12
12
12
N
1
-12.47
0.60
125.10
112.63
B
B
B
C6
N1
C2
DG
DG
DG
12
12
12
N
1
13.02
0.60
123.90
136.92
B
B
B
N1
C2
N3
DG
DG
DG
12
12
12
N
1
-4.22
0.50
128.60
124.38
B
B
B
N3
C4
C5
DG
DG
DG
12
12
12
N
1
5.73
0.50
111.50
117.23
B
B
B
C5
C6
N1
DG
DG
DG
12
12
12
N
1
2.85
0.40
106.40
109.25
B
B
B
C8
N9
C4
DG
DG
DG
12
12
12
N
1
6.16
0.60
126.00
132.16
B
B
B
N3
C4
N9
DG
DG
DG
12
12
12
N
1
-16.53
0.70
119.90
103.37
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
1
-7.31
0.60
128.60
121.29
B
B
B
C5
C6
O6
DG
DG
DG
12
12
12
N
1
A
A
C4'
C3'
DG
DG
2
2
0.107
0.010
1.529
1.636
N
1
A
A
C3'
C2'
DG
DG
2
2
-0.062
0.008
1.516
1.454
N
1
A
A
C2'
C1'
DG
DG
2
2
0.127
0.010
1.519
1.646
N
1
A
A
O4'
C1'
DG
DG
2
2
0.082
0.011
1.420
1.502
N
1
A
A
C1'
N9
DG
DG
2
2
-0.142
0.014
1.468
1.326
N
1
A
A
N1
C2
DG
DG
2
2
-0.066
0.008
1.373
1.307
N
1
A
A
C2
N3
DG
DG
2
2
-0.048
0.008
1.323
1.275
N
1
A
A
N7
C8
DG
DG
2
2
0.051
0.006
1.305
1.356
N
1
A
A
C2
N2
DG
DG
2
2
-0.090
0.010
1.341
1.251
N
1
A
A
O3'
P
DG
DU
2
3
0.089
0.012
1.607
1.696
Y
1
A
A
C2'
C1'
DU
DU
3
3
0.144
0.010
1.519
1.663
N
1
A
A
O4'
C1'
DA
DA
4
4
0.136
0.011
1.420
1.556
N
1
A
A
C4
C5
DA
DA
4
4
-0.065
0.007
1.383
1.318
N
1
A
A
N7
C8
DA
DA
4
4
0.043
0.007
1.311
1.354
N
1
A
A
C8
N9
DA
DA
4
4
-0.071
0.008
1.373
1.302
N
1
A
A
C6
N6
DA
DA
4
4
0.077
0.008
1.335
1.412
N
1
A
A
P
O5'
DG
DG
6
6
0.083
0.010
1.593
1.676
N
1
A
A
C5'
C4'
DG
DG
6
6
0.082
0.007
1.512
1.594
N
1
A
A
C4'
C3'
DG
DG
6
6
-0.108
0.010
1.521
1.413
N
1
A
A
C3'
C2'
DG
DG
6
6
-0.077
0.008
1.516
1.439
N
1
A
A
N1
C2
DG
DG
6
6
-0.072
0.008
1.373
1.301
N
1
A
A
C2
N3
DG
DG
6
6
0.053
0.008
1.323
1.376
N
1
A
A
C4
C5
DG
DG
6
6
-0.063
0.007
1.379
1.316
N
1
A
A
C5
N7
DG
DG
6
6
0.056
0.006
1.388
1.444
N
1
A
A
C8
N9
DG
DG
6
6
-0.068
0.007
1.374
1.306
N
1
B
B
O3'
P
5CM
DG
7
8
-0.084
0.012
1.607
1.523
Y
1
B
B
C4'
C3'
DG
DG
8
8
0.134
0.010
1.529
1.663
N
1
B
B
C3'
C2'
DG
DG
8
8
-0.069
0.008
1.516
1.447
N
1
B
B
C2'
C1'
DG
DG
8
8
-0.109
0.010
1.518
1.409
N
1
B
B
O4'
C1'
DG
DG
8
8
0.083
0.011
1.420
1.503
N
1
B
B
N7
C8
DG
DG
8
8
0.080
0.006
1.305
1.385
N
1
B
B
C8
N9
DG
DG
8
8
-0.045
0.007
1.374
1.329
N
1
B
B
N9
C4
DG
DG
8
8
0.081
0.008
1.375
1.456
N
1
B
B
C2
N2
DG
DG
8
8
-0.076
0.010
1.341
1.265
N
1
B
B
C5'
C4'
DU
DU
9
9
0.048
0.007
1.512
1.560
N
1
B
B
C2'
C1'
DU
DU
9
9
0.086
0.010
1.519
1.605
N
1
B
B
O3'
C3'
DU
DU
9
9
-0.061
0.006
1.419
1.358
N
1
B
B
C1'
N1
DU
DU
9
9
0.119
0.013
1.488
1.607
N
1
B
B
N1
C2
DU
DU
9
9
-0.063
0.009
1.381
1.318
N
1
B
B
P
OP2
DA
DA
10
10
-0.113
0.017
1.485
1.372
N
1
B
B
P
O5'
DA
DA
10
10
0.088
0.010
1.593
1.681
N
1
B
B
C5'
C4'
DA
DA
10
10
-0.080
0.011
1.509
1.429
N
1
B
B
C1'
N9
DA
DA
10
10
-0.089
0.014
1.468
1.379
N
1
B
B
C2
N3
DA
DA
10
10
0.058
0.009
1.331
1.389
N
1
B
B
C6
N6
DA
DA
10
10
0.049
0.008
1.335
1.384
N
1
B
B
P
O5'
DG
DG
12
12
0.082
0.010
1.593
1.675
N
1
B
B
C3'
C2'
DG
DG
12
12
-0.050
0.008
1.516
1.466
N
1
B
B
O4'
C4'
DG
DG
12
12
-0.102
0.010
1.446
1.344
N
1
B
B
O3'
C3'
DG
DG
12
12
-0.099
0.006
1.419
1.320
N
1
B
B
N1
C2
DG
DG
12
12
-0.064
0.008
1.373
1.309
N
1
B
B
N7
C8
DG
DG
12
12
0.050
0.006
1.305
1.355
N
1
B
B
C8
N9
DG
DG
12
12
-0.047
0.007
1.374
1.327
N
0.208
1.300
2870
1
ZDFB06 IN WHICH THE METHYL GROUPS OF THE THYMINE BASES WERE REMOVED FROM THE C5 POSITIONS.
TR
isotropic
TR
isotropic
TR
isotropic
1.300
49
304
17
238
0
fix
fix
fix
1.300
1D41
3869
2870
2.000
1
refinement
NUCLSQ
STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
covale
1.643
both
A
5CM
1
A
O3'
5CM
1
1_555
A
DG
2
A
P
DG
2
1_555
covale
1.615
both
A
DA
4
A
O3'
DA
4
1_555
A
5CM
5
A
P
5CM
5
1_555
covale
1.616
both
A
5CM
5
A
O3'
5CM
5
1_555
A
DG
6
A
P
DG
6
1_555
covale
1.523
both
B
5CM
7
B
O3'
5CM
1
1_555
B
DG
8
B
P
DG
2
1_555
covale
1.626
both
B
DA
10
B
O3'
DA
4
1_555
B
5CM
11
B
P
5CM
5
1_555
covale
1.604
both
B
5CM
11
B
O3'
5CM
5
1_555
B
DG
12
B
P
DG
6
1_555
metalc
2.124
A
HOH
69
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
metalc
2.076
A
HOH
71
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
metalc
2.050
A
HOH
72
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
metalc
2.189
A
HOH
73
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
metalc
2.079
A
HOH
74
E
O
HOH
1_555
B
MG
14
D
MG
MG
1_555
metalc
1.968
B
DU
9
B
OP2
DU
3
1_555
B
MG
13
C
MG
MG
1_555
metalc
2.051
B
MG
13
C
MG
MG
1_555
B
HOH
64
F
O
HOH
1_555
metalc
2.090
B
MG
13
C
MG
MG
1_555
B
HOH
65
F
O
HOH
1_555
metalc
2.240
B
MG
13
C
MG
MG
1_555
B
HOH
66
F
O
HOH
1_555
metalc
2.024
B
MG
13
C
MG
MG
1_555
B
HOH
67
F
O
HOH
1_555
metalc
2.180
B
MG
13
C
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
metalc
2.171
B
MG
14
D
MG
MG
1_555
B
HOH
70
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
5CM
1
A
N3
5CM
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
5CM
1
A
N4
5CM
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
5CM
1
A
O2
5CM
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
5CM
11
B
N3
5CM
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
5CM
11
B
O2
5CM
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
5CM
11
B
N4
5CM
5
1_555
hydrog
WATSON-CRICK
A
DU
3
A
N3
DU
3
1_555
B
DA
10
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DU
3
A
O4
DU
3
1_555
B
DA
10
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DU
9
B
N3
DU
3
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DU
9
B
O4
DU
3
1_555
hydrog
WATSON-CRICK
A
5CM
5
A
N3
5CM
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
5CM
5
A
N4
5CM
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
5CM
5
A
O2
5CM
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
5CM
7
B
N3
5CM
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
5CM
7
B
O2
5CM
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
5CM
7
B
N4
5CM
1
1_555
DNA
Z-DNA, DOUBLE HELIX, MODIFIED, DNA
1D41
PDB
1
1D41
1
6
1D41
1
6
1D41
A
1
1
6
7
12
1D41
7
12
1D41
B
1
1
6
BINDING SITE FOR RESIDUE MG B 13
B
MG
13
Software
6
BINDING SITE FOR RESIDUE MG B 14
B
MG
14
Software
6
B
DU
9
B
DU
3
6
1_555
B
HOH
64
F
HOH
6
1_555
B
HOH
65
F
HOH
6
1_555
B
HOH
66
F
HOH
6
1_555
B
HOH
67
F
HOH
6
1_555
B
HOH
68
F
HOH
6
1_555
A
HOH
69
E
HOH
6
1_555
A
HOH
71
E
HOH
6
1_555
A
HOH
72
E
HOH
6
1_555
A
HOH
73
E
HOH
6
1_555
A
HOH
74
E
HOH
6
1_555
B
HOH
70
F
HOH
6
1_555
19
P 21 21 21