0.025973
0.014995
0.000000
0.000000
0.029991
0.000000
0.000000
0.000000
0.012881
0.00000
0.00000
0.00000
Robinson, H.
Gao, Y.-G.
Sanishvili, R.
Joachimiak, A.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
38.502
38.502
77.631
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
Mg 2
24.305
MAGNESIUM 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
MG
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
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
28
1760
1766
10.1093/nar/28.8.1760
10734195
Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.
2000
10.2210/pdb1dnz/pdb
pdb_00001dnz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
123
1
IMAGE PLATE
1999-05-05
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
3045.992
DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
1
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
36
nat
water
no
no
(DA)(DC)(DC)(DG)(DG)(DC)(DC)(DG)(DG)(DT)
ACCGGCCGGT
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.44
50.0
VAPOR DIFFUSION, SITTING DROP
6.5
MPD, CACODYLATE, MGCL2, SPERMINE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
CACODYLATE
1
SPERMINE
1
MGCL2
1
MPD
1
MPD
2
-5.470
1
20
A
1
A
10
-7.138
A_DA1:DT10_A
1
-14.267
-0.732
-0.026
-0.613
7.488
1
19
A
2
A
9
2.159
A_DC2:DG9_A
2
-12.995
0.211
0.145
-0.141
7.265
1
19
A
3
A
8
0.221
A_DC3:DG8_A
3
-12.771
0.143
-0.038
-0.083
11.275
1
19
A
4
A
7
2.010
A_DG4:DC7_A
4
-9.851
-0.214
0.380
-0.118
2.426
1
19
A
5
A
6
0.338
A_DG5:DC6_A
5
-19.532
-0.340
0.154
-0.096
-2.426
1
19
A
6
A
5
0.338
A_DC6:DG5_A
6
-19.532
0.340
0.154
-0.096
-11.275
1
19
A
7
A
4
2.010
A_DC7:DG4_A
7
-9.851
0.214
0.380
-0.118
-7.265
1
19
A
8
A
3
0.221
A_DG8:DC3_A
8
-12.771
-0.143
-0.038
-0.083
-7.488
1
19
A
9
A
2
2.159
A_DG9:DC2_A
9
-12.995
-0.211
0.145
-0.141
5.470
1
20
A
10
A
1
-7.138
A_DT10:DA1_A
10
-14.267
0.732
-0.026
-0.613
2.551
38.092
A
A
1
2
12.188
A
A
10
9
2.902
7.898
0.874
-1.211
AA_DA1DC2:DG9DT10_AA
1
-2.057
3.174
37.239
-2.700
-1.559
3.012
34.815
A
A
2
3
9.380
A
A
9
8
3.268
5.589
-0.200
-1.406
AA_DC2DC3:DG8DG9_AA
2
-0.478
0.802
34.374
-3.172
0.265
2.149
27.761
A
A
3
4
24.260
A
A
8
7
3.097
11.244
-0.278
-1.719
AA_DC3DG4:DC7DG8_AA
3
-5.181
11.179
24.896
-5.879
-0.479
2.939
35.755
A
A
4
5
13.201
A
A
7
6
3.289
8.034
-0.568
-1.379
AA_DG4DG5:DC6DC7_AA
4
-2.333
3.834
34.794
-3.365
0.600
3.140
36.189
A
A
5
6
7.711
A
A
6
5
3.328
4.777
0.000
-1.262
AA_DG5DC6:DG5DC6_AA
5
0.000
0.000
35.883
-2.699
0.000
2.939
35.755
A
A
6
7
13.201
A
A
5
4
3.289
8.034
0.568
-1.379
AA_DC6DC7:DG4DG5_AA
6
2.333
-3.834
34.794
-3.365
-0.600
2.149
27.761
A
A
7
8
24.260
A
A
4
3
3.097
11.244
0.278
-1.719
AA_DC7DG8:DC3DG4_AA
7
5.181
-11.179
24.896
-5.879
0.479
3.012
34.815
A
A
8
9
9.380
A
A
3
2
3.268
5.589
0.200
-1.406
AA_DG8DG9:DC2DC3_AA
8
0.478
-0.802
34.374
-3.172
-0.265
2.551
38.092
A
A
9
10
12.188
A
A
2
1
2.902
7.898
-0.874
-1.211
AA_DG9DT10:DA1DC2_AA
9
2.057
-3.174
37.239
-2.700
1.559
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
1
0
2000-04-10
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-12-17
REL
REL
MG
MAGNESIUM ION
HOH
water
MO6
21
2
MG
MG
21
A
MO6
22
2
MG
MG
22
A
HOH
101
3
HOH
HOH
101
A
HOH
102
3
HOH
HOH
102
A
HOH
103
3
HOH
HOH
103
A
HOH
104
3
HOH
HOH
104
A
HOH
105
3
HOH
HOH
105
A
HOH
106
3
HOH
HOH
106
A
HOH
107
3
HOH
HOH
107
A
HOH
108
3
HOH
HOH
108
A
HOH
109
3
HOH
HOH
109
A
HOH
110
3
HOH
HOH
110
A
HOH
111
3
HOH
HOH
111
A
HOH
112
3
HOH
HOH
112
A
HOH
113
3
HOH
HOH
113
A
HOH
114
3
HOH
HOH
114
A
HOH
115
3
HOH
HOH
115
A
HOH
116
3
HOH
HOH
116
A
HOH
117
3
HOH
HOH
117
A
HOH
118
3
HOH
HOH
118
A
HOH
119
3
HOH
HOH
119
A
HOH
120
3
HOH
HOH
120
A
HOH
121
3
HOH
HOH
121
A
HOH
122
3
HOH
HOH
122
A
HOH
123
3
HOH
HOH
123
A
HOH
124
3
HOH
HOH
124
A
MO6
21
3
HOH
HOH
125
A
MO6
21
3
HOH
HOH
126
A
MO6
21
3
HOH
HOH
127
A
MO6
21
3
HOH
HOH
128
A
MO6
21
3
HOH
HOH
129
A
MO6
21
3
HOH
HOH
130
A
MO6
22
3
HOH
HOH
131
A
MO6
22
3
HOH
HOH
132
A
MO6
22
3
HOH
HOH
133
A
MO6
22
3
HOH
HOH
134
A
MO6
22
3
HOH
HOH
135
A
MO6
22
3
HOH
HOH
136
A
A
1
n
1
DA
1
A
C
2
n
2
DC
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
G
5
n
5
DG
5
A
C
6
n
6
DC
6
A
C
7
n
7
DC
7
A
G
8
n
8
DG
8
A
G
9
n
9
DG
9
A
T
10
n
10
DT
10
A
0.2290000
0.2270000
0.2780000
242
5
4656
author_defined_assembly
2
dimeric
A
HOH
125
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
126
D
O
HOH
1_555
178.4
A
HOH
125
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
127
D
O
HOH
1_555
90.5
A
HOH
126
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
127
D
O
HOH
1_555
88.3
A
HOH
125
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
128
D
O
HOH
1_555
90.3
A
HOH
126
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
128
D
O
HOH
1_555
90.7
A
HOH
127
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
128
D
O
HOH
1_555
87.6
A
HOH
125
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
129
D
O
HOH
1_555
91.1
A
HOH
126
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
129
D
O
HOH
1_555
90.2
A
HOH
127
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
129
D
O
HOH
1_555
177.1
A
HOH
128
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
129
D
O
HOH
1_555
90.0
A
HOH
125
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
130
D
O
HOH
1_555
88.8
A
HOH
126
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
130
D
O
HOH
1_555
90.2
A
HOH
127
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
130
D
O
HOH
1_555
91.7
A
HOH
128
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
130
D
O
HOH
1_555
178.9
A
HOH
129
D
O
HOH
1_555
A
MG
21
B
MG
MG
1_555
A
HOH
130
D
O
HOH
1_555
90.7
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
102
D
O
HOH
11_555
75.6
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
131
D
O
HOH
1_555
73.2
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
131
D
O
HOH
1_555
12.3
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
1_555
106.0
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
1_555
167.3
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
1_555
179.2
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
11_555
89.1
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
11_555
78.0
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
11_555
90.1
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
11_555
89.5
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
1_555
152.4
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
1_555
83.7
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
1_555
90.2
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
1_555
90.3
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
1_555
68.5
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
122.8
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
121.0
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
111.7
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
69.1
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
144.8
A
HOH
133
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
83.6
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
111.1
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
101.1
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
90.6
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
90.1
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
159.1
A
HOH
133
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
90.6
A
HOH
133
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
22.3
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
157.8
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
85.2
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
90.3
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
90.3
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
75.8
A
HOH
133
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
7.3
A
HOH
133
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
76.8
A
HOH
134
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
83.3
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
26.9
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
96.2
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
89.9
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
89.6
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
110.5
A
HOH
133
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
179.0
A
HOH
133
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
97.3
A
HOH
134
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
90.4
A
HOH
134
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
173.7
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
69.2
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
79.3
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
89.8
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
89.5
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
20.7
A
HOH
133
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
89.2
A
HOH
133
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
157.2
A
HOH
134
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
179.5
A
HOH
134
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
96.5
A
HOH
135
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
89.8
A
HOH
101
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
98.9
A
HOH
102
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
157.5
A
HOH
131
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
167.7
A
HOH
132
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
11.5
A
HOH
132
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
80.2
A
HOH
133
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
93.1
A
HOH
133
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
80.5
A
HOH
134
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
101.2
A
HOH
134
D
O
HOH
11_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
94.5
A
HOH
135
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
86.6
A
HOH
136
D
O
HOH
1_555
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
78.4
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
11_555
-x+y,y,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
38.8155000000
1
A
DG
4
0.080
SIDE CHAIN
1
A
DG
8
0.051
SIDE CHAIN
1
A
DG
9
0.060
SIDE CHAIN
1
A
DT
10
0.059
SIDE CHAIN
1
-4.63
0.70
108.00
103.37
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
-2.46
0.40
104.50
102.04
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
-4.64
0.70
102.20
97.56
A
A
A
C4'
C3'
C2'
DC
DC
DC
3
3
3
N
1
-2.56
0.40
121.90
119.34
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
-4.44
0.70
102.20
97.76
A
A
A
C4'
C3'
C2'
DG
DG
DG
4
4
4
N
1
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
2.65
0.40
120.30
122.95
A
A
A
C6
N1
C2
DC
DC
DC
6
6
6
N
1
-5.07
0.70
118.00
112.93
A
A
A
N3
C4
N4
DC
DC
DC
6
6
6
N
1
-2.89
0.40
104.50
101.61
A
A
A
O4'
C4'
C3'
DG
DG
DG
9
9
9
N
0.2790000
0.2270000
0.2290000
0.2270000
1.6
20.0
963
245
4874
4874
907
5
99.6
RANDOM
1
A POSTERIORI
0.0
0.0
MOLECULAR REPLACEMENT
G.PARKINSON ET AL.
SHELXL SWAT OPTION
0
0
235.5
1.6
20.0
24
240
14
202
0
0.009
0.025
0.071
0.003
0.060
29.2
1.6
20.0
1DNZ
4901
4901
0.0
0.0
0.0420000
1
47.8
15.2
99.6
0.4890000
1.60
1.65
9.2
8.4
96.8
model building
X-PLOR
refinement
SHELXL-97
data scaling
d*TREK
phasing
X-PLOR
A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES
1
N
N
2
N
N
2
N
N
3
N
N
metalc
2.064
A
MG
21
B
MG
MG
1_555
A
HOH
125
D
O
HOH
1_555
metalc
2.070
A
MG
21
B
MG
MG
1_555
A
HOH
126
D
O
HOH
1_555
metalc
2.070
A
MG
21
B
MG
MG
1_555
A
HOH
127
D
O
HOH
1_555
metalc
2.061
A
MG
21
B
MG
MG
1_555
A
HOH
128
D
O
HOH
1_555
metalc
2.058
A
MG
21
B
MG
MG
1_555
A
HOH
129
D
O
HOH
1_555
metalc
2.050
A
MG
21
B
MG
MG
1_555
A
HOH
130
D
O
HOH
1_555
metalc
2.399
A
MG
22
C
MG
MG
1_555
A
HOH
101
D
O
HOH
1_555
metalc
2.477
A
MG
22
C
MG
MG
1_555
A
HOH
102
D
O
HOH
11_555
metalc
2.055
A
MG
22
C
MG
MG
1_555
A
HOH
131
D
O
HOH
1_555
metalc
2.059
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
1_555
metalc
1.548
A
MG
22
C
MG
MG
1_555
A
HOH
132
D
O
HOH
11_555
metalc
2.062
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
1_555
metalc
1.516
A
MG
22
C
MG
MG
1_555
A
HOH
133
D
O
HOH
11_555
metalc
2.052
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
1_555
metalc
2.871
A
MG
22
C
MG
MG
1_555
A
HOH
134
D
O
HOH
11_555
metalc
2.060
A
MG
22
C
MG
MG
1_555
A
HOH
135
D
O
HOH
1_555
metalc
2.067
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
1_555
metalc
2.736
A
MG
22
C
MG
MG
1_555
A
HOH
136
D
O
HOH
11_555
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
A
DT
10
A
N3
DT
10
11_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
A
DT
10
A
O4
DT
10
11_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
9
A
N1
DG
9
11_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
9
A
O6
DG
9
11_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
9
A
N2
DG
9
11_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
A
DG
8
A
N1
DG
8
11_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
A
DG
8
A
O6
DG
8
11_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
A
DG
8
A
N2
DG
8
11_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
7
A
N3
DC
7
11_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
7
A
O2
DC
7
11_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
7
A
N4
DC
7
11_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
A
DC
6
A
N3
DC
6
11_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
A
DC
6
A
O2
DC
6
11_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
A
DC
6
A
N4
DC
6
11_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
5
A
N1
DG
5
11_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
5
A
O6
DG
5
11_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
5
A
N2
DG
5
11_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
A
DG
4
A
N1
DG
4
11_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
A
DG
4
A
O6
DG
4
11_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
A
DG
4
A
N2
DG
4
11_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
A
DC
3
A
N3
DC
3
11_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
A
DC
3
A
O2
DC
3
11_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
A
DC
3
A
N4
DC
3
11_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
A
DC
2
A
N3
DC
2
11_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
A
DC
2
A
O2
DC
2
11_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
A
DC
2
A
N4
DC
2
11_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
A
DA
1
A
N1
DA
1
11_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
A
DA
1
A
N6
DA
1
11_555
DNA
DNA CONFORMATION, METAL IONS, DNA
1DNZ
PDB
1
1DNZ
1
10
1DNZ
1
10
1DNZ
A
1
1
10
BINDING SITE FOR RESIDUE MG A 21
A
MG
21
Software
6
BINDING SITE FOR RESIDUE MG A 22
A
MG
22
Software
12
A
HOH
125
D
HOH
6
1_555
A
HOH
126
D
HOH
6
1_555
A
HOH
127
D
HOH
6
1_555
A
HOH
128
D
HOH
6
1_555
A
HOH
129
D
HOH
6
1_555
A
HOH
130
D
HOH
6
1_555
A
HOH
101
D
HOH
12
1_555
A
HOH
102
D
HOH
12
11_555
A
HOH
131
D
HOH
12
1_555
A
HOH
132
D
HOH
12
11_555
A
HOH
132
D
HOH
12
1_555
A
HOH
133
D
HOH
12
1_555
A
HOH
133
D
HOH
12
11_555
A
HOH
134
D
HOH
12
11_555
A
HOH
134
D
HOH
12
1_555
A
HOH
135
D
HOH
12
1_555
A
HOH
136
D
HOH
12
11_555
A
HOH
136
D
HOH
12
1_555
178
hexagonal
P 61 2 2