0.040631
0.000000
0.009860
0.000000
0.031993
0.000000
0.000000
0.000000
0.032195
0.00000
0.00000
0.00000
Venkadesh, S.
Kannan, R.
Mandal, P.K.
Gautham, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
103.64
90.00
24.612
31.257
31.962
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
H2 O
18.015
WATER
non-polymer
Mn 2
54.938
MANGANESE (II) ION
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
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
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
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
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
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
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
H
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
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
MN
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
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
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
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
sing
N
76
N
doub
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
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
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
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
To be Published
0353
Crystal Structure of d(CACGCG).d(CGCGTG) with 10mM MnCl2
10.2210/pdb3fq5/pdb
pdb_00003fq5
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
IMAGE PLATE
2007-09-15
MARRESEARCH
Mirror
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
1794.206
5'-D(*CP*AP*CP*GP*CP*G)-3'
2
syn
polymer
1825.216
5'-D(*CP*GP*CP*GP*TP*G)-3'
2
syn
polymer
54.938
MANGANESE (II) ION
2
syn
non-polymer
18.015
water
12
nat
water
no
no
(DC)(DA)(DC)(DG)(DC)(DG)
CACGCG
A,C
polydeoxyribonucleotide
no
no
(DC)(DG)(DC)(DG)(DT)(DG)
CGCGTG
B,D
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
VAPOR DIFFUSION, HANGING DROP
6.99
50mM Sodium Cacodylate buffer, 10mM MnCl2, 1mM Spermine, 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
Sodium Cacodylate
1
MnCl2
1
Spermine
1
MPD
1
Sodium Cacodylate
2
MnCl2
2
MPD
2
3.089
1
19
A
1
B
12
2.831
A_DC1:DG12_B
1
2.311
-0.518
0.114
-0.224
-0.782
1
20
A
2
B
11
-0.295
A_DA2:DT11_B
2
-9.123
0.542
0.232
-0.492
7.837
1
19
A
3
B
10
-0.534
A_DC3:DG10_B
3
-5.768
0.003
-0.046
-0.139
0.265
1
19
A
4
B
9
2.527
A_DG4:DC9_B
4
2.889
0.853
0.581
-0.170
-1.250
1
19
A
5
B
8
4.872
A_DC5:DG8_B
5
4.426
-0.739
0.158
-0.351
1.482
1
19
A
6
B
7
2.530
A_DG6:DC7_B
6
1.526
0.047
0.283
-0.222
6.402
1
19
C
1
D
12
1.930
C_DC1:DG12_D
7
3.940
-0.665
-0.030
0.035
-3.531
1
20
C
2
D
11
11.666
C_DA2:DT11_D
8
-3.126
-0.081
0.165
-0.286
4.352
1
19
C
3
D
10
3.178
C_DC3:DG10_D
9
-3.322
0.259
0.353
-0.235
0.207
1
19
C
4
D
9
1.261
C_DG4:DC9_D
10
-0.200
0.535
0.515
-0.085
-0.231
1
19
C
6
D
7
4.414
C_DG6:DC7_D
11
-2.839
0.367
0.776
-0.286
5.108
-6.676
A
A
1
2
46.362
B
B
12
11
3.719
-4.514
-0.393
4.970
AA_DC1DA2:DT11DG12_BB
1
-3.454
-35.476
-3.503
-9.075
-29.083
3.380
-43.325
A
A
2
3
-0.455
B
B
11
10
3.363
0.336
-0.409
-1.091
AA_DA2DC3:DG10DT11_BB
2
1.076
1.458
-43.311
1.443
-0.446
5.015
-8.364
A
A
3
4
12.992
B
B
10
9
3.905
-1.855
0.591
5.406
AA_DC3DG4:DC9DG10_BB
3
-2.275
-15.939
-7.833
-30.075
-4.528
3.481
-56.479
A
A
4
5
2.126
B
B
9
8
3.544
-2.010
0.298
-0.964
AA_DG4DC5:DG8DC9_BB
4
4.264
4.510
-56.298
1.141
0.573
2.990
-11.395
A
A
5
6
-3.766
B
B
8
7
3.576
0.736
-0.203
5.514
AA_DC5DG6:DC7DG8_BB
5
-3.411
-17.460
-10.849
-28.862
-6.078
4.497
-9.443
C
C
1
2
7.197
D
D
12
11
3.851
-1.182
-0.062
5.410
CC_DC1DA2:DT11DG12_DD
6
0.222
1.353
-9.366
-29.684
0.222
3.293
-43.629
C
C
2
3
2.877
D
D
11
10
3.358
-2.137
-0.148
-1.187
CC_DA2DC3:DG10DT11_DD
7
-1.367
-1.840
-43.558
1.806
-0.332
4.819
-8.990
C
C
3
4
10.582
D
D
10
9
3.904
-1.643
0.297
5.386
CC_DC3DG4:DC9DG10_DD
8
-1.394
-8.982
-8.728
-29.214
-2.473
pdbx_entity_src_syn
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Data collection
Source and taxonomy
Data collection
Database references
Derived calculations
1
0
2009-02-10
1
1
2011-07-13
1
2
2019-08-28
1
3
2024-03-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
PDBJ
2009-01-07
REL
REL
MN
MANGANESE (II) ION
HOH
water
32630
synthetic construct
sample
32630
synthetic construct
sample
MN
1
3
MN
MN
7
A
MN
2
3
MN
MN
8
A
HOH
9
4
HOH
HOH
9
A
HOH
2
4
HOH
HOH
10
A
HOH
11
4
HOH
HOH
11
A
HOH
3
4
HOH
HOH
12
A
HOH
6
4
HOH
HOH
6
B
HOH
8
4
HOH
HOH
13
B
HOH
12
4
HOH
HOH
14
B
HOH
4
4
HOH
HOH
7
C
HOH
10
4
HOH
HOH
10
C
HOH
1
4
HOH
HOH
1
D
HOH
5
4
HOH
HOH
5
D
HOH
7
4
HOH
HOH
13
D
DC
1
n
1
DC
1
A
DA
2
n
2
DA
2
A
DC
3
n
3
DC
3
A
DG
4
n
4
DG
4
A
DC
5
n
5
DC
5
A
DG
6
n
6
DG
6
A
DC
7
n
1
DC
7
B
DG
8
n
2
DG
8
B
DC
9
n
3
DC
9
B
DG
10
n
4
DG
10
B
DT
11
n
5
DT
11
B
DG
12
n
6
DG
12
B
DC
1
n
1
DC
1
C
DA
2
n
2
DA
2
C
DC
3
n
3
DC
3
C
DG
4
n
4
DG
4
C
DC
5
n
5
DC
5
C
DG
6
n
6
DG
6
C
DC
7
n
1
DC
7
D
DG
8
n
2
DG
8
D
DC
9
n
3
DC
9
D
DG
10
n
4
DG
10
D
DT
11
n
5
DT
11
D
DG
12
n
6
DG
12
D
author_and_software_defined_assembly
PISA
2
dimeric
author_and_software_defined_assembly
PISA
2
dimeric
650
-6
2320
610
-5
2410
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
C
C
O3'
P
DA
DC
2
3
1.85
1
-4.83
0.80
105.90
101.07
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
1
-5.15
0.70
108.00
102.85
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.81
0.40
121.90
126.71
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
-5.24
0.50
117.40
112.16
A
A
A
C4
C5
C6
DC
DC
DC
1
1
1
N
1
4.02
0.50
121.00
125.02
A
A
A
C5
C6
N1
DC
DC
DC
1
1
1
N
1
-4.10
0.60
118.90
114.80
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
6.38
0.70
121.90
128.28
A
A
A
N3
C2
O2
DC
DC
DC
1
1
1
N
1
4.38
0.70
118.00
122.38
A
A
A
N3
C4
N4
DC
DC
DC
1
1
1
N
1
-9.31
0.70
120.20
110.89
A
A
A
C5
C4
N4
DC
DC
DC
1
1
1
N
1
-19.48
1.90
104.00
84.52
A
A
A
O3'
P
O5'
DC
DA
DA
1
2
2
Y
1
12.79
1.20
110.70
123.49
A
A
A
O5'
P
OP1
DA
DA
DA
2
2
2
N
1
-8.80
0.90
105.70
96.90
A
A
A
O5'
P
OP2
DA
DA
DA
2
2
2
N
1
-7.40
0.80
109.40
102.00
A
A
A
O5'
C5'
C4'
DA
DA
DA
2
2
2
N
1
-8.23
0.40
104.50
96.27
A
A
A
O4'
C4'
C3'
DA
DA
DA
2
2
2
N
1
-5.40
0.80
123.70
118.30
A
A
A
C5
C6
N6
DA
DA
DA
2
2
2
N
1
15.04
1.90
104.00
119.04
A
A
A
O3'
P
O5'
DA
DC
DC
2
3
3
Y
1
-7.49
0.90
105.70
98.21
A
A
A
O5'
P
OP2
DC
DC
DC
3
3
3
N
1
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-6.62
1.10
118.80
112.18
A
A
A
C2
N1
C1'
DC
DC
DC
3
3
3
N
1
9.52
1.20
110.70
120.22
A
A
A
O5'
P
OP2
DG
DG
DG
4
4
4
N
1
4.56
0.30
108.30
112.86
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
11.29
1.20
119.70
130.99
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
1
13.05
1.90
104.00
117.05
A
A
A
O3'
P
O5'
DG
DC
DC
4
5
5
Y
1
16.71
1.50
119.60
136.31
A
A
A
OP1
P
OP2
DC
DC
DC
5
5
5
N
1
-9.46
0.90
105.70
96.24
A
A
A
O5'
P
OP2
DC
DC
DC
5
5
5
N
1
9.19
1.10
109.80
118.99
A
A
A
C5'
C4'
O4'
DG
DG
DG
6
6
6
N
1
7.31
0.90
103.10
110.41
A
A
A
C4'
C3'
C2'
DG
DG
DG
6
6
6
N
1
4.62
0.50
106.80
111.42
A
A
A
O4'
C1'
C2'
DG
DG
DG
6
6
6
N
1
3.95
0.30
108.30
112.25
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
8.37
1.20
115.70
124.07
B
B
B
C5'
C4'
C3'
DC
DC
DC
7
7
7
N
1
2.64
0.40
120.30
122.94
B
B
B
C6
N1
C2
DC
DC
DC
7
7
7
N
1
-4.56
0.70
119.20
114.64
B
B
B
N1
C2
N3
DC
DC
DC
7
7
7
N
1
4.84
0.70
121.90
126.74
B
B
B
N3
C2
O2
DC
DC
DC
7
7
7
N
1
8.38
1.10
109.80
118.18
B
B
B
C5'
C4'
O4'
DG
DG
DG
8
8
8
N
1
3.20
0.50
128.60
131.80
B
B
B
N3
C4
C5
DG
DG
DG
8
8
8
N
1
5.72
0.40
110.80
116.52
B
B
B
C4
C5
N7
DG
DG
DG
8
8
8
N
1
-8.35
0.50
104.30
95.95
B
B
B
C5
N7
C8
DG
DG
DG
8
8
8
N
1
5.86
0.50
113.10
118.96
B
B
B
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-4.97
0.60
130.40
125.43
B
B
B
C6
C5
N7
DG
DG
DG
8
8
8
N
1
4.95
0.60
119.90
124.85
B
B
B
N1
C6
O6
DG
DG
DG
8
8
8
N
1
-3.76
0.60
128.60
124.84
B
B
B
C5
C6
O6
DG
DG
DG
8
8
8
N
1
-5.75
0.80
109.40
103.65
B
B
B
O5'
C5'
C4'
DC
DC
DC
9
9
9
N
1
-9.25
0.70
108.00
98.75
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.39
0.40
121.90
125.29
B
B
B
N3
C4
C5
DC
DC
DC
9
9
9
N
1
4.95
0.60
118.90
123.85
B
B
B
N1
C2
O2
DC
DC
DC
9
9
9
N
1
-6.37
0.70
121.90
115.53
B
B
B
N3
C2
O2
DC
DC
DC
9
9
9
N
1
-9.05
0.70
118.00
108.95
B
B
B
N3
C4
N4
DC
DC
DC
9
9
9
N
1
5.56
0.70
120.20
125.76
B
B
B
C5
C4
N4
DC
DC
DC
9
9
9
N
1
-10.07
0.80
109.40
99.33
B
B
B
O5'
C5'
C4'
DG
DG
DG
10
10
10
N
1
3.44
0.30
108.30
111.74
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
-4.04
0.60
125.10
121.06
B
B
B
C6
N1
C2
DG
DG
DG
10
10
10
N
1
-3.17
0.50
128.60
125.43
B
B
B
N3
C4
C5
DG
DG
DG
10
10
10
N
1
-3.46
0.40
110.80
107.34
B
B
B
C4
C5
N7
DG
DG
DG
10
10
10
N
1
4.59
0.50
104.30
108.89
B
B
B
C5
N7
C8
DG
DG
DG
10
10
10
N
1
-3.43
0.50
113.10
109.67
B
B
B
N7
C8
N9
DG
DG
DG
10
10
10
N
1
-5.61
0.70
119.90
114.29
B
B
B
N3
C2
N2
DG
DG
DG
10
10
10
N
1
2.04
0.30
108.30
110.34
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-4.86
0.60
118.00
113.14
B
B
B
C4
C5
C6
DT
DT
DT
11
11
11
N
1
5.33
0.60
123.70
129.03
B
B
B
C5
C6
N1
DT
DT
DT
11
11
11
N
1
6.83
0.60
119.00
125.83
B
B
B
C4
C5
C7
DT
DT
DT
11
11
11
N
1
-3.63
0.60
125.10
121.47
B
B
B
C6
N1
C2
DG
DG
DG
12
12
12
N
1
6.74
0.60
123.90
130.64
B
B
B
N1
C2
N3
DG
DG
DG
12
12
12
N
1
-3.31
0.50
111.90
108.59
B
B
B
C2
N3
C4
DG
DG
DG
12
12
12
N
1
3.88
0.40
105.40
109.28
B
B
B
N9
C4
C5
DG
DG
DG
12
12
12
N
1
-6.25
0.70
119.90
113.65
B
B
B
N3
C2
N2
DG
DG
DG
12
12
12
N
1
-12.11
1.90
109.30
97.19
C
C
C
C5'
C4'
O4'
DC
DC
DC
1
1
1
N
1
-11.53
0.80
102.40
90.87
C
C
C
C3'
C2'
C1'
DC
DC
DC
1
1
1
N
1
5.01
0.50
106.80
111.81
C
C
C
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
1
3.11
0.40
120.30
123.41
C
C
C
C6
N1
C2
DC
DC
DC
1
1
1
N
1
3.09
0.50
119.90
122.99
C
C
C
C2
N3
C4
DC
DC
DC
1
1
1
N
1
-2.96
0.40
121.90
118.94
C
C
C
N3
C4
C5
DC
DC
DC
1
1
1
N
1
6.09
0.60
118.90
124.99
C
C
C
N1
C2
O2
DC
DC
DC
1
1
1
N
1
10.82
1.50
119.60
130.42
C
C
C
OP1
P
OP2
DA
DA
DA
2
2
2
N
1
-16.96
0.90
105.70
88.74
C
C
C
O5'
P
OP1
DA
DA
DA
2
2
2
N
1
-6.21
0.40
104.50
98.29
C
C
C
O4'
C4'
C3'
DA
DA
DA
2
2
2
N
1
6.76
0.90
103.10
109.86
C
C
C
C4'
C3'
C2'
DA
DA
DA
2
2
2
N
1
-5.53
0.80
105.90
100.37
C
C
C
O4'
C1'
C2'
DA
DA
DA
2
2
2
N
1
-6.69
0.50
129.30
122.61
C
C
C
N1
C2
N3
DA
DA
DA
2
2
2
N
1
4.51
0.50
110.60
115.11
C
C
C
C2
N3
C4
DA
DA
DA
2
2
2
N
1
5.20
0.60
118.60
123.80
C
C
C
N1
C6
N6
DA
DA
DA
2
2
2
N
1
-5.92
0.80
123.70
117.78
C
C
C
C5
C6
N6
DA
DA
DA
2
2
2
N
1
-15.16
1.20
119.70
104.54
C
C
C
C3'
O3'
P
DA
DA
DC
2
2
3
Y
1
-7.43
0.80
102.40
94.97
C
C
C
C3'
C2'
C1'
DC
DC
DC
3
3
3
N
1
2.05
0.30
108.30
110.35
C
C
C
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
3.88
0.40
121.90
125.78
C
C
C
N3
C4
C5
DC
DC
DC
3
3
3
N
1
-6.06
0.50
117.40
111.34
C
C
C
C4
C5
C6
DC
DC
DC
3
3
3
N
1
3.80
0.50
121.00
124.80
C
C
C
C5
C6
N1
DC
DC
DC
3
3
3
N
1
-4.46
0.70
120.20
115.74
C
C
C
C5
C4
N4
DC
DC
DC
3
3
3
N
1
-12.32
1.90
104.00
91.68
C
C
C
O3'
P
O5'
DC
DG
DG
3
4
4
Y
1
-10.42
0.70
108.00
97.58
C
C
C
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-3.71
0.60
123.90
120.19
C
C
C
N1
C2
N3
DG
DG
DG
4
4
4
N
1
7.48
0.70
119.90
127.38
C
C
C
N3
C2
N2
DG
DG
DG
4
4
4
N
1
-6.33
0.90
105.70
99.37
C
C
C
O5'
P
OP2
DC
DC
DC
5
5
5
N
1
3.15
0.50
106.80
109.95
C
C
C
O4'
C1'
C2'
DC
DC
DC
5
5
5
N
1
2.46
0.40
121.90
124.36
C
C
C
N3
C4
C5
DC
DC
DC
5
5
5
N
1
-6.99
0.50
117.40
110.41
C
C
C
C4
C5
C6
DC
DC
DC
5
5
5
N
1
5.49
0.50
121.00
126.49
C
C
C
C5
C6
N1
DC
DC
DC
5
5
5
N
1
-6.24
0.60
118.90
112.66
C
C
C
N1
C2
O2
DC
DC
DC
5
5
5
N
1
8.82
0.70
121.90
130.72
C
C
C
N3
C2
O2
DC
DC
DC
5
5
5
N
1
4.54
0.70
118.00
122.54
C
C
C
N3
C4
N4
DC
DC
DC
5
5
5
N
1
-7.11
0.70
120.20
113.09
C
C
C
C5
C4
N4
DC
DC
DC
5
5
5
N
1
-11.99
1.90
104.00
92.01
C
C
C
O3'
P
O5'
DC
DG
DG
5
6
6
Y
1
7.94
1.10
110.50
118.44
C
C
C
O3'
P
OP1
DC
DG
DG
5
6
6
Y
1
4.22
0.70
110.30
114.52
C
C
C
C1'
O4'
C4'
DG
DG
DG
6
6
6
N
1
3.62
0.60
118.80
122.42
C
C
C
C4
C5
C6
DG
DG
DG
6
6
6
N
1
-3.80
0.40
106.40
102.60
C
C
C
C8
N9
C4
DG
DG
DG
6
6
6
N
1
3.35
0.40
105.40
108.75
C
C
C
N9
C4
C5
DG
DG
DG
6
6
6
N
1
-3.90
0.60
130.40
126.50
C
C
C
C6
C5
N7
DG
DG
DG
6
6
6
N
1
-7.37
1.00
110.10
102.73
D
D
D
C1'
O4'
C4'
DC
DC
DC
7
7
7
N
1
-3.94
0.50
117.40
113.46
D
D
D
C4
C5
C6
DC
DC
DC
7
7
7
N
1
4.59
0.50
121.00
125.59
D
D
D
C5
C6
N1
DC
DC
DC
7
7
7
N
1
6.61
0.60
118.90
125.51
D
D
D
N1
C2
O2
DC
DC
DC
7
7
7
N
1
6.86
1.10
118.80
125.66
D
D
D
C2
N1
C1'
DC
DC
DC
7
7
7
N
1
8.98
1.20
110.70
119.68
D
D
D
O5'
P
OP1
DG
DG
DG
8
8
8
N
1
-5.90
0.90
105.70
99.80
D
D
D
O5'
P
OP2
DG
DG
DG
8
8
8
N
1
-6.57
0.80
109.40
102.83
D
D
D
O5'
C5'
C4'
DG
DG
DG
8
8
8
N
1
-4.22
0.70
108.00
103.78
D
D
D
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
3.70
0.50
111.90
115.60
D
D
D
C2
N3
C4
DG
DG
DG
8
8
8
N
1
4.45
0.50
111.50
115.95
D
D
D
C5
C6
N1
DG
DG
DG
8
8
8
N
1
-4.99
0.60
128.60
123.61
D
D
D
C5
C6
O6
DG
DG
DG
8
8
8
N
1
11.49
1.20
119.70
131.19
D
D
D
C3'
O3'
P
DG
DG
DC
8
8
9
Y
1
15.23
1.90
104.00
119.23
D
D
D
O3'
P
O5'
DG
DC
DC
8
9
9
Y
1
11.37
1.50
119.60
130.97
D
D
D
OP1
P
OP2
DC
DC
DC
9
9
9
N
1
-7.01
0.90
105.70
98.69
D
D
D
O5'
P
OP2
DC
DC
DC
9
9
9
N
1
8.25
1.20
119.70
127.95
D
D
D
C3'
O3'
P
DC
DC
DG
9
9
10
Y
1
-7.45
0.80
109.40
101.95
D
D
D
O5'
C5'
C4'
DG
DG
DG
10
10
10
N
1
-8.01
1.00
110.10
102.09
D
D
D
C1'
O4'
C4'
DG
DG
DG
10
10
10
N
1
-4.48
0.50
113.10
108.62
D
D
D
N7
C8
N9
DG
DG
DG
10
10
10
N
1
2.77
0.40
106.40
109.17
D
D
D
C8
N9
C4
DG
DG
DG
10
10
10
N
1
-2.43
0.40
104.50
102.07
D
D
D
O4'
C4'
C3'
DT
DT
DT
11
11
11
N
1
-4.81
0.80
105.90
101.09
D
D
D
O4'
C1'
C2'
DT
DT
DT
11
11
11
N
1
-4.22
0.70
124.90
120.68
D
D
D
C5
C4
O4
DT
DT
DT
11
11
11
N
1
-5.97
0.60
119.00
113.03
D
D
D
C4
C5
C7
DT
DT
DT
11
11
11
N
1
7.54
0.60
122.90
130.44
D
D
D
C6
C5
C7
DT
DT
DT
11
11
11
N
1
-6.78
0.80
109.40
102.62
D
D
D
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
-16.08
2.50
109.40
93.32
D
D
D
C2'
C3'
O3'
DG
DG
DG
12
12
12
N
1
2.94
0.30
108.30
111.24
D
D
D
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
5.28
0.50
111.90
117.18
D
D
D
C2
N3
C4
DG
DG
DG
12
12
12
N
1
-3.01
0.50
113.10
110.09
D
D
D
N7
C8
N9
DG
DG
DG
12
12
12
N
1
3.98
0.60
130.40
134.38
D
D
D
C6
C5
N7
DG
DG
DG
12
12
12
N
1
7.06
0.90
116.20
123.26
D
D
D
N1
C2
N2
DG
DG
DG
12
12
12
N
1
A
A
C4
C5
DC
DC
1
1
-0.053
0.008
1.425
1.372
N
1
A
A
N3
C4
DA
DA
2
2
-0.036
0.006
1.344
1.308
N
1
A
A
N7
C8
DA
DA
2
2
0.051
0.007
1.311
1.362
N
1
A
A
O3'
C3'
DG
DG
4
4
-0.088
0.006
1.419
1.331
N
1
A
A
N7
C8
DG
DG
4
4
0.037
0.006
1.305
1.342
N
1
A
A
O3'
C3'
DC
DC
5
5
-0.067
0.006
1.419
1.352
N
1
A
A
O3'
C3'
DG
DG
6
6
-0.075
0.006
1.419
1.344
N
1
B
B
C5'
C4'
DC
DC
7
7
0.043
0.007
1.512
1.555
N
1
B
B
N1
C6
DC
DC
7
7
-0.047
0.006
1.367
1.320
N
1
B
B
C4
C5
DC
DC
7
7
-0.054
0.008
1.425
1.371
N
1
B
B
N7
C8
DG
DG
8
8
0.041
0.006
1.305
1.346
N
1
B
B
C8
N9
DG
DG
8
8
0.050
0.007
1.374
1.424
N
1
B
B
O3'
C3'
DG
DG
10
10
-0.055
0.006
1.419
1.364
N
1
B
B
N9
C4
DG
DG
10
10
0.051
0.008
1.375
1.426
N
1
B
B
P
O5'
DT
DT
11
11
0.075
0.010
1.593
1.668
N
1
B
B
C1'
N1
DT
DT
11
11
0.104
0.013
1.488
1.592
N
1
B
B
C6
N1
DG
DG
12
12
-0.071
0.007
1.391
1.320
N
1
B
B
C5
N7
DG
DG
12
12
0.057
0.006
1.388
1.445
N
1
B
B
N7
C8
DG
DG
12
12
0.038
0.006
1.305
1.343
N
1
C
C
O3'
P
DC
DA
1
2
0.082
0.012
1.607
1.689
Y
1
C
C
P
O5'
DA
DA
2
2
0.062
0.010
1.593
1.655
N
1
C
C
C1'
N9
DA
DA
2
2
-0.090
0.014
1.468
1.378
N
1
C
C
C6
N1
DA
DA
2
2
0.043
0.007
1.351
1.394
N
1
C
C
O3'
P
DA
DC
2
3
0.243
0.012
1.607
1.850
Y
1
C
C
P
O5'
DC
DC
3
3
0.068
0.010
1.593
1.661
N
1
C
C
C4
C5
DC
DC
3
3
-0.067
0.008
1.425
1.358
N
1
C
C
N7
C8
DG
DG
4
4
0.043
0.006
1.305
1.348
N
1
C
C
O3'
C3'
DC
DC
5
5
-0.110
0.006
1.419
1.309
N
1
C
C
N1
C2
DC
DC
5
5
-0.068
0.010
1.397
1.329
N
1
C
C
O3'
C3'
DG
DG
6
6
-0.073
0.006
1.419
1.346
N
1
C
C
N7
C8
DG
DG
6
6
0.064
0.006
1.305
1.369
N
1
D
D
N3
C4
DG
DG
8
8
0.046
0.007
1.350
1.396
N
1
D
D
C6
N1
DG
DG
8
8
0.047
0.007
1.391
1.438
N
1
D
D
O3'
C3'
DC
DC
9
9
-0.108
0.006
1.419
1.311
N
1
D
D
C4
C5
DG
DG
10
10
-0.047
0.007
1.379
1.332
N
1
D
D
O3'
C3'
DT
DT
11
11
-0.073
0.006
1.419
1.346
N
1
D
D
C5
C6
DT
DT
11
11
0.053
0.007
1.339
1.392
N
1
D
D
C6
N1
DT
DT
11
11
0.044
0.007
1.378
1.422
N
1
D
D
C5
C7
DT
DT
11
11
0.039
0.006
1.496
1.535
N
1
D
D
O3'
C3'
DG
DG
12
12
-0.059
0.006
1.419
1.360
N
1
D
D
C4
C5
DG
DG
12
12
-0.076
0.007
1.379
1.303
N
12.018
0.17
0.00
-0.01
-0.15
0.00
-0.03
0.974
0.939
0.20162
0.16485
0.16692
2.80
14.71
61
1108
5.2
97.01
12.551
0.248
RANDOM
1
Isotropic
THROUGHOUT
MOLECULAR REPLACEMENT
0.388
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
0.327
2.80
14.71
12
494
2
480
0
0.031
0.021
536
4.456
3.000
820
0.152
0.200
92
0.023
0.020
252
0.235
0.200
196
0.341
0.200
279
0.115
0.200
14
0.294
0.200
22
0.021
0.200
1
4.122
3.000
793
4.896
4.500
820
0.202
0.295
2.870
1
77
72
20
95.12
42.5
2.8
15.0
3FQ5
1241
1179
1.0
0.042
0.042
1
8.0
2.88
95
0.129
2.80
2.87
3.3
72
0.1149
3.25
94.8
data collection
MAR345dtb
phasing
PHASER
refinement
REFMAC
5.2.0019
data reduction
AUTOMAR
data scaling
SCALEPACK
N
Crystal Structure of d(CACGCG).d(CGCGTG) with 10mM MnCl2
1
N
N
2
N
N
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
metalc
2.229
A
MN
8
F
MN
MN
1_555
A
HOH
10
G
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
11
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
11
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
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
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
7
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
7
B
N4
DC
1
1_555
hydrog
WATSON-CRICK
C
DC
1
C
N3
DC
1
1_555
D
DG
12
D
N1
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
1
C
N4
DC
1
1_555
D
DG
12
D
O6
DG
6
1_555
hydrog
WATSON-CRICK
C
DC
1
C
O2
DC
1
1_555
D
DG
12
D
N2
DG
6
1_555
hydrog
WATSON-CRICK
C
DA
2
C
N1
DA
2
1_555
D
DT
11
D
N3
DT
5
1_555
hydrog
WATSON-CRICK
C
DA
2
C
N6
DA
2
1_555
D
DT
11
D
O4
DT
5
1_555
hydrog
WATSON-CRICK
C
DC
3
C
N3
DC
3
1_555
D
DG
10
D
N1
DG
4
1_555
hydrog
WATSON-CRICK
C
DC
3
C
N4
DC
3
1_555
D
DG
10
D
O6
DG
4
1_555
hydrog
WATSON-CRICK
C
DC
3
C
O2
DC
3
1_555
D
DG
10
D
N2
DG
4
1_555
hydrog
WATSON-CRICK
C
DG
4
C
N1
DG
4
1_555
D
DC
9
D
N3
DC
3
1_555
hydrog
WATSON-CRICK
C
DG
4
C
N2
DG
4
1_555
D
DC
9
D
O2
DC
3
1_555
hydrog
WATSON-CRICK
C
DG
4
C
O6
DG
4
1_555
D
DC
9
D
N4
DC
3
1_555
hydrog
WATSON-CRICK
C
DC
5
C
N3
DC
5
1_555
D
DG
8
D
N1
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
5
C
N4
DC
5
1_555
D
DG
8
D
O6
DG
2
1_555
hydrog
WATSON-CRICK
C
DC
5
C
O2
DC
5
1_555
D
DG
8
D
N2
DG
2
1_555
hydrog
WATSON-CRICK
C
DG
6
C
N1
DG
6
1_555
D
DC
7
D
N3
DC
1
1_555
hydrog
WATSON-CRICK
C
DG
6
C
N2
DG
6
1_555
D
DC
7
D
O2
DC
1
1_555
hydrog
WATSON-CRICK
C
DG
6
C
O6
DG
6
1_555
D
DC
7
D
N4
DC
1
1_555
DNA
Double helix, DNA
3FQ5
PDB
1
3FQ5
3FQ5
PDB
2
3FQ5
1
6
3FQ5
1
6
3FQ5
A
1
1
6
1
6
3FQ5
1
6
3FQ5
C
1
1
6
7
12
3FQ5
7
12
3FQ5
B
2
1
6
7
12
3FQ5
7
12
3FQ5
D
2
1
6
BINDING SITE FOR RESIDUE MN A 7
A
MN
7
Software
3
BINDING SITE FOR RESIDUE MN A 8
A
MN
8
Software
2
A
DA
2
A
DA
2
3
1_555
A
HOH
9
G
HOH
3
1_555
D
DG
10
D
DG
4
3
1_555
A
DG
4
A
DG
4
2
1_555
A
HOH
10
G
HOH
2
1_555
4
P 1 21 1