0.047733
0.000000
0.000000
0.000000
0.016166
0.000000
0.000000
0.000000
0.014601
0.00000
0.00000
0.00000
Gao, Y.-G.
Robinson, H.
Sanishvili, R.
Joachimiak, A.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
20.950
61.860
68.490
C9 H12 Br N2 O8 P
387.078
n
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
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
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
Na 1
22.990
SODIUM ION
non-polymer
C10 H26 N4
202.340
SPERMINE
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
O
N
8
N
O
N
9
N
BR
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
O
N
35
N
P
N
36
N
O
N
37
N
O
N
38
N
O
N
39
N
C
N
40
R
C
N
41
N
O
N
42
S
C
N
43
N
O
N
44
N
C
N
45
R
C
Y
46
N
N
Y
47
N
C
Y
48
N
N
Y
49
N
C
Y
50
N
C
N
51
N
N
Y
52
N
N
Y
53
N
C
Y
54
N
N
Y
55
N
C
N
56
N
H
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
O
N
71
N
P
N
72
N
O
N
73
N
O
N
74
N
O
N
75
N
C
N
76
R
C
N
77
N
O
N
78
S
C
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
N
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
C
N
87
N
N
N
88
N
C
N
89
N
C
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
O
N
105
N
P
N
106
N
O
N
107
N
O
N
108
N
O
N
109
N
C
N
110
R
C
N
111
N
O
N
112
S
C
N
113
N
O
N
114
N
C
N
115
R
C
Y
116
N
N
Y
117
N
C
Y
118
N
N
Y
119
N
C
N
120
N
C
N
121
N
O
N
122
N
N
N
123
N
C
N
124
N
N
N
125
N
N
Y
126
N
C
N
127
N
H
N
128
N
H
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
O
N
142
N
H
N
143
N
H
N
144
N
MG
N
145
N
NA
N
146
N
N
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
N
N
151
N
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
N
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
N
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
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
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
N
38
N
sing
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
Y
58
N
sing
Y
59
N
sing
Y
60
N
doub
N
61
N
sing
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
doub
N
67
N
sing
N
68
N
sing
Y
69
N
sing
Y
70
N
doub
N
71
N
sing
Y
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
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
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
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
Y
131
N
sing
Y
132
N
sing
Y
133
N
doub
N
134
N
sing
Y
135
N
sing
N
136
N
sing
Y
137
N
doub
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
38
16452
16460
10.1021/bi9914614
10600106
Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
1999
10.2210/pdb1dcr/pdb
pdb_00001dcr
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
IMAGE PLATE
1996-06-17
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
3158.913
5'-D(*CP*CP*GP*AP*AP*(BRU)P*GP*AP*GP*G)-3'
2
syn
polymer
202.340
SPERMINE
1
syn
non-polymer
24.305
MAGNESIUM ION
3
syn
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
87
nat
water
no
yes
(DC)(DC)(DG)(DA)(DA)(BRU)(DG)(DA)(DG)(DG)
CCGAAUGAGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
1.76
29.96
VAPOR DIFFUSION, SITTING DROP
7.5
MPD, MGCL2, TRIS, SPERMINE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
SPERMINE
1
MGCL2
1
TRIS
1
MPD
1
MPD
2
-3.185
1
19
A
2
B
19
-3.243
A_DC2:DG19_B
1
2.432
0.162
-0.101
-0.107
32.112
9
11
A
3
B
18
-3.230
A_DG3:DA18_B
2
4.379
6.718
0.530
-4.499
-34.108
9
11
A
4
B
17
4.071
A_DA4:DG17_B
3
-7.028
-6.564
0.543
-4.428
-1.458
1
20
A
5
B
16
0.694
A_DA5:BRU16_B
4
8.583
0.043
-0.209
-0.058
3.541
1
20
A
6
B
15
-1.053
A_BRU6:DA15_B
5
5.731
0.115
0.002
-0.066
40.713
9
11
A
7
B
14
6.863
A_DG7:DA14_B
6
-7.007
6.552
1.122
-4.081
-37.797
9
11
A
8
B
13
5.816
A_DA8:DG13_B
7
1.738
-6.531
0.760
-4.146
-2.291
1
19
A
9
B
12
-5.970
A_DG9:DC12_B
8
6.023
-0.235
-0.193
-0.200
-0.916
1
19
A
10
B
11
-5.662
A_DG10:DC11_B
9
-6.397
-0.078
0.092
-0.249
3.004
62.400
A
A
2
3
2.418
B
B
19
18
2.959
2.504
0.388
1.687
AA_DC2DG3:DA18DG19_BB
1
-2.238
2.161
62.319
1.524
-0.467
4.243
-8.233
A
A
3
4
9.664
B
B
18
17
4.946
-1.316
0.440
-1.071
AA_DG3DA4:DG17DA18_BB
2
-4.174
-30.650
-6.975
12.993
-14.479
3.149
66.343
A
A
4
5
4.417
B
B
17
16
3.031
4.830
-0.682
2.105
AA_DA4DA5:BRU16DG17_BB
3
1.175
-1.075
66.177
1.742
0.668
3.443
26.199
A
A
5
6
-0.652
B
B
16
15
3.449
-0.295
0.169
-0.531
AA_DA5BRU6:DA15BRU16_BB
4
-1.189
2.625
26.171
-1.088
-0.711
3.119
65.798
A
A
6
7
5.703
B
B
15
14
2.991
6.187
0.731
1.920
AA_BRU6DG7:DA14DA15_BB
5
-2.157
1.988
65.508
1.532
-0.755
2.190
-8.795
A
A
7
8
47.759
B
B
14
13
5.275
-6.241
-0.211
-1.274
AA_DG7DA8:DG13DA14_BB
6
3.654
27.959
-5.008
30.297
11.496
3.043
59.161
A
A
8
9
6.061
B
B
13
12
2.878
5.975
-0.163
1.962
AA_DA8DG9:DC12DG13_BB
7
1.156
-1.173
58.876
1.710
0.218
3.515
38.452
A
A
9
10
10.971
B
B
12
11
3.506
7.162
-0.752
-0.021
AA_DG9DG10:DC11DC12_BB
8
-5.621
8.611
37.398
-1.002
0.381
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
1999-11-19
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2023-08-09
_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.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_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.ptnr1_symmetry
_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.ptnr2_symmetry
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-11-05
REL
REL
SPM
SPERMINE
MG
MAGNESIUM ION
NA
SODIUM ION
HOH
water
1D9R
PDB STRUCTURE 1D9R
PDB
experimental model
SPM
24
2
SPM
SPM
24
A
MO5
21
3
MG
MG
21
A
MO5
22
3
MG
MG
22
A
NA
25
4
NA
NA
25
B
MO4
23
3
MG
MG
23
B
HOH
1004
5
HOH
HOH
1004
A
HOH
1005
5
HOH
HOH
1005
A
HOH
1006
5
HOH
HOH
1006
A
HOH
1011
5
HOH
HOH
1011
A
HOH
1012
5
HOH
HOH
1012
A
HOH
1013
5
HOH
HOH
1013
A
HOH
1015
5
HOH
HOH
1015
A
HOH
1017
5
HOH
HOH
1017
A
HOH
1018
5
HOH
HOH
1018
A
HOH
1021
5
HOH
HOH
1021
A
HOH
1023
5
HOH
HOH
1023
A
HOH
1026
5
HOH
HOH
1026
A
HOH
1030
5
HOH
HOH
1030
A
HOH
1031
5
HOH
HOH
1031
A
HOH
1034
5
HOH
HOH
1034
A
HOH
1036
5
HOH
HOH
1036
A
HOH
1037
5
HOH
HOH
1037
A
HOH
1038
5
HOH
HOH
1038
A
HOH
1041
5
HOH
HOH
1041
A
HOH
1042
5
HOH
HOH
1042
A
HOH
1045
5
HOH
HOH
1045
A
HOH
1046
5
HOH
HOH
1046
A
HOH
1048
5
HOH
HOH
1048
A
HOH
1050
5
HOH
HOH
1050
A
HOH
1051
5
HOH
HOH
1051
A
HOH
1052
5
HOH
HOH
1052
A
HOH
1054
5
HOH
HOH
1054
A
HOH
1055
5
HOH
HOH
1055
A
HOH
1058
5
HOH
HOH
1058
A
HOH
1059
5
HOH
HOH
1059
A
HOH
1060
5
HOH
HOH
1060
A
HOH
1061
5
HOH
HOH
1061
A
HOH
1063
5
HOH
HOH
1063
A
HOH
1064
5
HOH
HOH
1064
A
HOH
1065
5
HOH
HOH
1065
A
HOH
1069
5
HOH
HOH
1069
A
HOH
1072
5
HOH
HOH
1072
A
HOH
1073
5
HOH
HOH
1073
A
HOH
1074
5
HOH
HOH
1074
A
HOH
1075
5
HOH
HOH
1075
A
HOH
1076
5
HOH
HOH
1076
A
HOH
1077
5
HOH
HOH
1077
A
MO5
21
5
HOH
HOH
1078
A
MO5
21
5
HOH
HOH
1079
A
MO5
21
5
HOH
HOH
1080
A
MO5
21
5
HOH
HOH
1081
A
MO5
21
5
HOH
HOH
1082
A
MO5
22
5
HOH
HOH
1083
A
MO5
22
5
HOH
HOH
1084
A
MO5
22
5
HOH
HOH
1085
A
MO5
22
5
HOH
HOH
1086
A
MO5
22
5
HOH
HOH
1087
A
HOH
1001
5
HOH
HOH
1001
B
HOH
1003
5
HOH
HOH
1003
B
HOH
1007
5
HOH
HOH
1007
B
HOH
1008
5
HOH
HOH
1008
B
HOH
1009
5
HOH
HOH
1009
B
HOH
1010
5
HOH
HOH
1010
B
HOH
1014
5
HOH
HOH
1014
B
HOH
1016
5
HOH
HOH
1016
B
HOH
1019
5
HOH
HOH
1019
B
HOH
1020
5
HOH
HOH
1020
B
HOH
1022
5
HOH
HOH
1022
B
HOH
1024
5
HOH
HOH
1024
B
HOH
1025
5
HOH
HOH
1025
B
HOH
1027
5
HOH
HOH
1027
B
HOH
1028
5
HOH
HOH
1028
B
HOH
1032
5
HOH
HOH
1032
B
HOH
1033
5
HOH
HOH
1033
B
HOH
1039
5
HOH
HOH
1039
B
HOH
1040
5
HOH
HOH
1040
B
HOH
1043
5
HOH
HOH
1043
B
HOH
1044
5
HOH
HOH
1044
B
HOH
1047
5
HOH
HOH
1047
B
HOH
1049
5
HOH
HOH
1049
B
HOH
1053
5
HOH
HOH
1053
B
HOH
1056
5
HOH
HOH
1056
B
HOH
1062
5
HOH
HOH
1062
B
HOH
1066
5
HOH
HOH
1066
B
HOH
1067
5
HOH
HOH
1067
B
HOH
1068
5
HOH
HOH
1068
B
HOH
1070
5
HOH
HOH
1070
B
HOH
1071
5
HOH
HOH
1071
B
MO4
23
5
HOH
HOH
1088
B
MO4
23
5
HOH
HOH
1089
B
MO4
23
5
HOH
HOH
1090
B
MO4
23
5
HOH
HOH
1091
B
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
+U
6
n
6
BRU
6
A
G
7
n
7
DG
7
A
A
8
n
8
DA
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
C
11
n
1
DC
11
B
C
12
n
2
DC
12
B
G
13
n
3
DG
13
B
A
14
n
4
DA
14
B
A
15
n
5
DA
15
B
+U
16
n
6
BRU
16
B
G
17
n
7
DG
17
B
A
18
n
8
DA
18
B
G
19
n
9
DG
19
B
G
20
n
10
DG
20
B
0.192
0.187
0.261
278
5
5409
author_defined_assembly
2
dimeric
A
DG
9
A
N7
DG
9
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1083
H
O
HOH
1_555
87.2
A
DG
9
A
N7
DG
9
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1084
H
O
HOH
1_555
94.5
A
HOH
1083
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1084
H
O
HOH
1_555
178.0
A
DG
9
A
N7
DG
9
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1085
H
O
HOH
1_555
84.6
A
HOH
1083
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1085
H
O
HOH
1_555
90.1
A
HOH
1084
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1085
H
O
HOH
1_555
90.9
A
DG
9
A
N7
DG
9
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1086
H
O
HOH
1_555
172.8
A
HOH
1083
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1086
H
O
HOH
1_555
89.7
A
HOH
1084
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1086
H
O
HOH
1_555
88.7
A
HOH
1085
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1086
H
O
HOH
1_555
88.9
A
DG
9
A
N7
DG
9
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1087
H
O
HOH
1_555
97.0
A
HOH
1083
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1087
H
O
HOH
1_555
90.4
A
HOH
1084
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1087
H
O
HOH
1_555
88.5
A
HOH
1085
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1087
H
O
HOH
1_555
178.3
A
HOH
1086
H
O
HOH
1_555
A
MG
22
E
MG
MG
1_555
A
HOH
1087
H
O
HOH
1_555
89.5
A
DG
10
A
OP1
DG
10
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1078
H
O
HOH
1_555
93.5
A
DG
10
A
OP1
DG
10
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1079
H
O
HOH
1_555
85.2
A
HOH
1078
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1079
H
O
HOH
1_555
178.4
A
DG
10
A
OP1
DG
10
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1080
H
O
HOH
1_555
91.8
A
HOH
1078
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1080
H
O
HOH
1_555
88.4
A
HOH
1079
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1080
H
O
HOH
1_555
90.6
A
DG
10
A
OP1
DG
10
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1081
H
O
HOH
1_555
175.7
A
HOH
1078
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1081
H
O
HOH
1_555
90.8
A
HOH
1079
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1081
H
O
HOH
1_555
90.6
A
HOH
1080
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1081
H
O
HOH
1_555
88.8
A
DG
10
A
OP1
DG
10
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1082
H
O
HOH
1_555
89.6
A
HOH
1078
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1082
H
O
HOH
1_555
90.9
A
HOH
1079
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1082
H
O
HOH
1_555
90.1
A
HOH
1080
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1082
H
O
HOH
1_555
178.5
A
HOH
1081
H
O
HOH
1_555
A
MG
21
D
MG
MG
1_555
A
HOH
1082
H
O
HOH
1_555
89.8
B
BRU
16
B
OP1
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
B
BRU
16
B
O5'
BRU
6
1_555
35.5
B
BRU
16
B
OP1
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
B
BRU
16
B
OP2
BRU
6
1_555
33.3
B
BRU
16
B
O5'
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
B
BRU
16
B
OP2
BRU
6
1_555
62.1
B
BRU
16
B
OP1
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
B
HOH
1014
I
O
HOH
1_555
140.1
B
BRU
16
B
O5'
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
B
HOH
1014
I
O
HOH
1_555
126.9
B
BRU
16
B
OP2
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
B
HOH
1014
I
O
HOH
1_555
156.8
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
DG
20
B
OP1
DG
10
3_555
175.6
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
1_555
99.4
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
1_555
80.6
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
3_555
80.6
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
3_555
99.4
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
3_555
179.6
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
1_555
80.6
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
1_555
99.4
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
1_555
179.6
B
HOH
1088
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
1_555
0.0
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
3_555
99.4
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
3_555
80.6
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
3_555
0.0
B
HOH
1088
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
3_555
179.6
B
HOH
1089
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
3_555
179.6
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
92.2
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
92.2
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
90.2
B
HOH
1088
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
90.2
B
HOH
1089
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
90.2
B
HOH
1089
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
90.2
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
92.2
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
92.2
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
90.2
B
HOH
1088
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
90.2
B
HOH
1089
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
90.2
B
HOH
1089
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
90.2
B
HOH
1090
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
0.0
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
87.8
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
87.8
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
89.8
B
HOH
1088
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
89.8
B
HOH
1089
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
89.8
B
HOH
1089
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
89.8
B
HOH
1090
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
180.0
B
HOH
1090
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
180.0
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
87.8
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
87.8
B
HOH
1088
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
89.8
B
HOH
1088
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
89.8
B
HOH
1089
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
89.8
B
HOH
1089
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
89.8
B
HOH
1090
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
180.0
B
HOH
1090
I
O
HOH
3_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
179.9
B
HOH
1091
I
O
HOH
1_555
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
0.0
A
BRU
6
A
BRU
6
DU
B
BRU
16
B
BRU
6
DU
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
B
MG
23
G
MG
1
A
HOH
1042
H
HOH
1
B
HOH
1024
I
HOH
1
B
HOH
1070
I
HOH
1
B
HOH
1090
I
HOH
1
B
HOH
1091
I
HOH
1
A
DA
8
0.094
SIDE CHAIN
1
B
DC
11
0.087
SIDE CHAIN
1
B
DA
14
0.069
SIDE CHAIN
1
11.55
1.20
119.70
131.25
A
A
A
C3'
O3'
P
BRU
BRU
DG
6
6
7
Y
1
-6.91
0.90
105.70
98.79
A
A
A
O5'
P
OP2
DG
DG
DG
7
7
7
N
1
-4.44
0.70
108.00
103.56
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.54
0.30
108.30
112.84
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
6.38
0.30
108.30
114.68
B
B
B
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
3.98
0.30
108.30
112.28
B
B
B
O4'
C1'
N9
DA
DA
DA
14
14
14
N
1
3.05
0.50
117.70
120.75
B
B
B
C5
C6
N1
DA
DA
DA
15
15
15
N
1
-5.19
0.50
129.30
124.11
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
4.90
0.60
118.60
123.50
B
B
B
N1
C6
N6
DA
DA
DA
18
18
18
N
SHELX-97 OPTIONS HOPE
0.266
0.196
0.191
1.60
20.0
2055
291
5771
5409
1837
5
98.4
RANDOM
1
THROUGHOUT
0.0
0.0
MOLECULAR REPLACEMENT
PDB STRUCTURE 1D9R
PARKINSON ET AL.
SHELX-97 OPTIONS SWAT
1.60
20.0
77
523
34
412
0
0.009
0.025
0.067
0.072
0.066
32.7
1.60
20.0
1DCR
5771
5771
0
0
0.075
1
19.2
2.61
94.8
0.445
1.60
1.66
3.80
2.10
93.7
model building
X-PLOR
refinement
SHELXL-97
data scaling
d*TREK
phasing
X-PLOR
CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
3
N
N
5
N
N
5
N
N
covale
1.609
both
A
DA
5
A
O3'
DA
5
1_555
A
BRU
6
A
P
BRU
6
1_555
covale
1.576
both
A
BRU
6
A
O3'
BRU
6
1_555
A
DG
7
A
P
DG
7
1_555
covale
1.619
both
B
DA
15
B
O3'
DA
5
1_555
B
BRU
16
B
P
BRU
6
1_555
covale
1.597
both
B
BRU
16
B
O3'
BRU
6
1_555
B
DG
17
B
P
DG
7
1_555
metalc
2.307
A
DG
9
A
N7
DG
9
1_555
A
MG
22
E
MG
MG
1_555
metalc
2.117
A
DG
10
A
OP1
DG
10
1_555
A
MG
21
D
MG
MG
1_555
metalc
2.061
A
MG
21
D
MG
MG
1_555
A
HOH
1078
H
O
HOH
1_555
metalc
2.055
A
MG
21
D
MG
MG
1_555
A
HOH
1079
H
O
HOH
1_555
metalc
2.068
A
MG
21
D
MG
MG
1_555
A
HOH
1080
H
O
HOH
1_555
metalc
2.061
A
MG
21
D
MG
MG
1_555
A
HOH
1081
H
O
HOH
1_555
metalc
2.059
A
MG
21
D
MG
MG
1_555
A
HOH
1082
H
O
HOH
1_555
metalc
2.056
A
MG
22
E
MG
MG
1_555
A
HOH
1083
H
O
HOH
1_555
metalc
2.069
A
MG
22
E
MG
MG
1_555
A
HOH
1084
H
O
HOH
1_555
metalc
2.069
A
MG
22
E
MG
MG
1_555
A
HOH
1085
H
O
HOH
1_555
metalc
2.067
A
MG
22
E
MG
MG
1_555
A
HOH
1086
H
O
HOH
1_555
metalc
2.063
A
MG
22
E
MG
MG
1_555
A
HOH
1087
H
O
HOH
1_555
metalc
4.103
B
BRU
16
B
OP1
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
metalc
2.542
B
BRU
16
B
O5'
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
metalc
2.104
B
BRU
16
B
OP2
BRU
6
1_555
B
NA
25
F
NA
NA
1_555
metalc
2.029
B
DG
20
B
OP1
DG
10
1_555
B
MG
23
G
MG
MG
1_555
metalc
2.028
B
DG
20
B
OP1
DG
10
3_555
B
MG
23
G
MG
MG
1_555
metalc
2.056
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
1_555
metalc
2.057
B
MG
23
G
MG
MG
1_555
B
HOH
1088
I
O
HOH
3_555
metalc
2.057
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
1_555
metalc
2.056
B
MG
23
G
MG
MG
1_555
B
HOH
1089
I
O
HOH
3_555
metalc
2.062
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
1_555
metalc
2.062
B
MG
23
G
MG
MG
1_555
B
HOH
1090
I
O
HOH
3_555
metalc
2.062
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
1_555
metalc
2.062
B
MG
23
G
MG
MG
1_555
B
HOH
1091
I
O
HOH
3_555
metalc
2.908
B
NA
25
F
NA
NA
1_555
B
HOH
1014
I
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N2
DG
3
1_555
B
DA
18
B
N7
DA
8
1_555
hydrog
TYPE_11_PAIR
A
DG
3
A
N3
DG
3
1_555
B
DA
18
B
N6
DA
8
1_555
hydrog
TYPE_11_PAIR
A
DA
4
A
N6
DA
4
1_555
B
DG
17
B
N3
DG
7
1_555
hydrog
TYPE_11_PAIR
A
DA
4
A
N7
DA
4
1_555
B
DG
17
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
BRU
16
B
N3
BRU
6
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
BRU
16
B
O4
BRU
6
1_555
hydrog
WATSON-CRICK
A
BRU
6
A
N3
BRU
6
1_555
B
DA
15
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
BRU
6
A
O4
BRU
6
1_555
B
DA
15
B
N6
DA
5
1_555
hydrog
TYPE_11_PAIR
A
DG
7
A
N2
DG
7
1_555
B
DA
14
B
N7
DA
4
1_555
hydrog
TYPE_11_PAIR
A
DG
7
A
N3
DG
7
1_555
B
DA
14
B
N6
DA
4
1_555
hydrog
TYPE_11_PAIR
A
DA
8
A
N6
DA
8
1_555
B
DG
13
B
N3
DG
3
1_555
hydrog
TYPE_11_PAIR
A
DA
8
A
N7
DA
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
12
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
12
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
12
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
11
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
11
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
11
B
N4
DC
1
1_555
DNA
TANDEM GA BASE PAIRS, GA MISMATCH, DEOXYRIBONUCLEIC ACID, DNA
1DCR
PDB
1
1DCR
1
10
1DCR
1
10
1DCR
A
1
1
10
11
20
1DCR
11
20
1DCR
B
1
1
10
BINDING SITE FOR RESIDUE SPM A 24
A
SPM
24
Software
10
BINDING SITE FOR RESIDUE NA B 25
B
NA
25
Software
3
BINDING SITE FOR RESIDUE MG A 21
A
MG
21
Software
6
BINDING SITE FOR RESIDUE MG A 22
A
MG
22
Software
6
BINDING SITE FOR RESIDUE MG B 23
B
MG
23
Software
10
A
DG
7
A
DG
7
10
1_555
A
DG
7
A
DG
7
10
3_655
A
HOH
1069
H
HOH
10
1_555
A
HOH
1069
H
HOH
10
3_655
B
DC
12
B
DC
2
10
3_655
B
DC
12
B
DC
2
10
1_555
B
DG
13
B
DG
3
10
1_555
B
DG
13
B
DG
3
10
3_655
B
HOH
1056
I
HOH
10
3_655
B
HOH
1056
I
HOH
10
1_555
B
DA
15
B
DA
5
3
1_555
B
BRU
16
B
BRU
6
3
1_555
B
HOH
1014
I
HOH
3
1_555
A
DG
10
A
DG
10
6
1_555
A
HOH
1078
H
HOH
6
1_555
A
HOH
1079
H
HOH
6
1_555
A
HOH
1080
H
HOH
6
1_555
A
HOH
1081
H
HOH
6
1_555
A
HOH
1082
H
HOH
6
1_555
A
DG
9
A
DG
9
6
1_555
A
HOH
1083
H
HOH
6
1_555
A
HOH
1084
H
HOH
6
1_555
A
HOH
1085
H
HOH
6
1_555
A
HOH
1086
H
HOH
6
1_555
A
HOH
1087
H
HOH
6
1_555
B
DG
20
B
DG
10
10
1_555
B
DG
20
B
DG
10
10
3_555
B
HOH
1088
I
HOH
10
1_555
B
HOH
1088
I
HOH
10
3_555
B
HOH
1089
I
HOH
10
3_555
B
HOH
1089
I
HOH
10
1_555
B
HOH
1090
I
HOH
10
1_555
B
HOH
1090
I
HOH
10
3_555
B
HOH
1091
I
HOH
10
3_555
B
HOH
1091
I
HOH
10
1_555
20
orthorhombic
C 2 2 21