0.042333
0.000000
0.000000
0.000000
0.025720
0.000000
0.000000
0.000000
0.015959
0.00000
0.00000
0.00000
Munnur, D.G.
Mitchell, E.P.
Forsyth, V.T.
Teixeira, S.C.M.
Neidle, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
23.622
38.881
62.660
C21 H18 N6
354.408
2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE
DB921
non-polymer
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
Y
1
N
C
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
Y
10
N
C
Y
11
N
C
Y
12
N
C
Y
13
N
C
Y
14
N
N
Y
15
N
C
Y
16
N
C
Y
17
N
N
Y
18
N
C
Y
19
N
C
Y
20
N
C
Y
21
N
C
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
C
N
26
N
N
N
27
N
N
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
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
O
N
47
N
P
N
48
N
O
N
49
N
O
N
50
N
O
N
51
N
C
N
52
R
C
N
53
N
O
N
54
S
C
N
55
N
O
N
56
N
C
N
57
R
C
Y
58
N
N
Y
59
N
C
Y
60
N
N
Y
61
N
C
Y
62
N
C
N
63
N
N
Y
64
N
N
Y
65
N
C
Y
66
N
N
Y
67
N
C
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
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
O
N
83
N
P
N
84
N
O
N
85
N
O
N
86
N
O
N
87
N
C
N
88
R
C
N
89
N
O
N
90
S
C
N
91
N
O
N
92
N
C
N
93
R
C
N
94
N
N
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
C
N
99
N
N
N
100
N
C
N
101
N
C
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
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
O
N
117
N
P
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
C
N
122
R
C
N
123
N
O
N
124
S
C
N
125
N
O
N
126
N
C
N
127
R
C
Y
128
N
N
Y
129
N
C
Y
130
N
N
Y
131
N
C
N
132
N
C
N
133
N
O
N
134
N
N
N
135
N
C
N
136
N
N
N
137
N
N
Y
138
N
C
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
O
N
154
N
P
N
155
N
O
N
156
N
O
N
157
N
O
N
158
N
C
N
159
R
C
N
160
N
O
N
161
S
C
N
162
N
O
N
163
N
C
N
164
R
C
N
165
N
N
N
166
N
C
N
167
N
O
N
168
N
N
N
169
N
C
N
170
N
O
N
171
N
C
N
172
N
C
N
173
N
C
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
186
N
H
N
187
N
H
N
188
N
H
N
189
N
O
N
190
N
H
N
191
N
H
N
192
N
MG
Y
1
N
doub
Y
2
N
sing
N
3
N
sing
Y
4
N
sing
N
5
N
sing
Y
6
N
doub
Y
7
N
sing
Y
8
N
sing
N
9
N
sing
Y
10
N
doub
N
11
N
sing
N
12
N
sing
Y
13
N
doub
Y
14
N
sing
Y
15
N
sing
N
16
N
sing
Y
17
N
doub
N
18
N
sing
Y
19
N
sing
Y
20
N
sing
Y
21
N
doub
N
22
N
sing
N
23
N
sing
Y
24
N
doub
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
Y
28
N
sing
Y
29
N
sing
Y
30
N
sing
N
31
N
sing
Y
32
N
doub
N
33
N
sing
Y
34
N
doub
N
35
N
sing
Y
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
E
doub
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
doub
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
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
Y
72
N
sing
Y
73
N
sing
Y
74
N
doub
N
75
N
sing
Y
76
N
sing
Y
77
N
sing
Y
78
N
doub
N
79
N
sing
Y
80
N
doub
N
81
N
sing
N
82
N
sing
Y
83
N
sing
Y
84
N
doub
N
85
N
sing
Y
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
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
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
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
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
doub
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
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
Y
145
N
sing
Y
146
N
sing
Y
147
N
doub
N
148
N
sing
Y
149
N
sing
N
150
N
sing
Y
151
N
doub
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
doub
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
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
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
doub
N
191
N
sing
N
192
N
sing
N
193
N
doub
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
To be Published
0353
A Detailed Study of Water Network in the Minor Groove of D(Cgcgaattcgcg)2 and D(Cgcaaatttgcg)2 in Presence of Linear Groove Binders
10.2210/pdb4ah1/pdb
pdb_00004ah1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
TOROIDAL MIRROR
CCD
2009-07-19
MARMOSAIC 225 mm CCD
SI (111)
SINGLE WAVELENGTH
M
x-ray
1
0.873
1.0
ID23-2
ESRF
0.873
SYNCHROTRON
ESRF BEAMLINE ID23-2
3662.404
5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*GP)-3'
2
syn
polymer
354.408
2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
109
nat
water
no
no
(DC)(DG)(DC)(DA)(DA)(DA)(DT)(DT)(DT)(DG)(DC)(DG)
CGCAAATTTGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
1.97
57.91
NONE
VAPOR DIFFUSION, SITTING DROP
6.5
MAGNESIUM CHLORIDE, DNA, DB921, MPD, SPERMINE TETRAHYDROCHLORIDE, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 285 K, PH 6.50
285
-2.634
1
19
A
1
B
24
-0.615
A_DC1:DG24_B
1
17.376
0.150
-0.130
-0.205
-9.803
1
19
A
2
B
23
-5.194
A_DG2:DC23_B
2
-24.138
-0.140
0.455
-0.227
-6.434
1
19
A
3
B
22
2.687
A_DC3:DG22_B
3
-3.313
0.188
0.071
-0.123
12.507
1
20
A
4
B
21
-1.527
A_DA4:DT21_B
4
-15.849
-0.085
-0.137
-0.134
9.454
1
20
A
5
B
20
2.395
A_DA5:DT20_B
5
-18.690
0.046
-0.020
-0.145
4.499
1
20
A
6
B
19
9.610
A_DA6:DT19_B
6
-22.359
-0.059
0.158
-0.003
-3.126
1
20
A
7
B
18
8.616
A_DT7:DA18_B
7
-20.546
-0.115
0.106
-0.062
-8.856
1
20
A
8
B
17
3.631
A_DT8:DA17_B
8
-17.367
-0.036
0.132
-0.192
-11.831
1
20
A
9
B
16
-4.607
A_DT9:DA16_B
9
-13.732
-0.333
-0.037
-0.036
11.213
1
19
A
10
B
15
5.686
A_DG10:DC15_B
10
-1.349
-0.127
0.174
-0.076
4.870
1
19
A
11
B
14
-0.393
A_DC11:DG14_B
11
-18.609
0.189
0.181
-0.168
-1.284
1
19
A
12
B
13
0.637
A_DG12:DC13_B
12
-17.445
-0.262
0.074
-0.186
3.467
41.454
A
A
1
2
-19.801
B
B
24
23
3.763
-13.757
-0.806
0.471
AA_DC1DG2:DC23DG24_BB
1
-3.371
4.852
39.059
2.340
0.729
3.223
42.713
A
A
2
3
-13.007
B
B
23
22
3.363
-9.387
0.741
0.582
AA_DG2DC3:DG22DC23_BB
2
4.520
-6.264
41.481
1.762
-0.553
3.100
28.156
A
A
3
4
7.986
B
B
22
21
3.047
3.866
-0.665
1.239
AA_DC3DA4:DT21DG22_BB
3
2.992
-6.181
27.737
1.689
2.030
3.289
37.985
A
A
4
5
0.521
B
B
21
20
3.288
0.339
0.145
0.304
AA_DA4DA5:DT20DT21_BB
4
-0.535
0.822
37.980
0.423
-0.292
3.188
36.328
A
A
5
6
6.241
B
B
20
19
3.246
3.882
0.460
-0.073
AA_DA5DA6:DT19DT20_BB
5
-2.260
3.634
36.058
-0.652
-1.050
3.299
31.215
A
A
6
7
3.154
B
B
19
18
3.332
1.696
0.005
-0.532
AA_DA6DT7:DA18DT19_BB
6
0.323
-0.601
31.168
-1.315
0.053
3.250
37.478
A
A
7
8
7.787
B
B
18
17
3.307
4.989
-0.354
-0.170
AA_DT7DT8:DA17DA18_BB
7
0.811
-1.266
37.148
-0.923
0.658
3.217
38.040
A
A
8
9
-5.378
B
B
17
16
3.252
-3.500
-0.396
0.051
AA_DT8DT9:DA16DA17_BB
8
1.530
-2.351
37.855
0.519
0.800
2.783
31.245
A
A
9
10
-2.631
B
B
16
15
2.966
-1.413
0.925
1.070
AA_DT9DG10:DC15DA16_BB
9
-3.854
7.176
30.981
2.224
-2.362
3.305
44.140
A
A
10
11
-11.098
B
B
15
14
3.458
-8.294
-1.138
0.758
AA_DG10DC11:DG14DC15_BB
10
-1.659
2.220
43.362
1.821
1.352
3.395
33.038
A
A
11
12
16.107
B
B
14
13
3.435
9.048
0.211
0.302
AA_DC11DG12:DC13DG14_BB
11
0.819
-1.458
31.798
-1.101
-0.223
database_PDB_rev
database_PDB_rev_record
exptl_crystal_grow
pdbx_database_proc
pdbx_database_status
pdbx_seq_map_depositor_info
struct_biol
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Data collection
Experimental preparation
Other
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2013-01-16
1
1
2019-01-30
1
2
2023-12-20
_exptl_crystal_grow.method
_exptl_crystal_grow.temp
_pdbx_database_status.recvd_author_approval
_pdbx_seq_map_depositor_info.one_letter_code_mod
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_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.pdbx_dist_value
_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.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
CRYSTAL STRUCTURE OF THE DB 985-D(CGCAAATTTGCG)2 COMPLEX AT 1.20 A RESOLUTION
CRYSTAL STRUCTURE OF THE DB 985-D(CGCGAATTCGCG)2 COMPLEX AT 1.25 A RESOLUTION.
PDBE
Y
PDBE
2012-02-02
REL
REL
1
B
O
HOH
2001
6.28
D2A
2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE
MG
MAGNESIUM ION
HOH
water
32630
SYNTHETIC CONSTRUCT
sample
1S2R
PDB ENTRY 1S2R
PDB
experimental model
D2A
1013
2
D2A
D2A
1013
A
MG
2000
3
MG
MG
2000
B
HOH
2001
4
HOH
HOH
2001
A
HOH
2002
4
HOH
HOH
2002
A
HOH
2003
4
HOH
HOH
2003
A
HOH
2004
4
HOH
HOH
2004
A
HOH
2005
4
HOH
HOH
2005
A
HOH
2006
4
HOH
HOH
2006
A
HOH
2007
4
HOH
HOH
2007
A
HOH
2008
4
HOH
HOH
2008
A
HOH
2009
4
HOH
HOH
2009
A
HOH
2010
4
HOH
HOH
2010
A
HOH
2011
4
HOH
HOH
2011
A
HOH
2012
4
HOH
HOH
2012
A
HOH
2013
4
HOH
HOH
2013
A
HOH
2014
4
HOH
HOH
2014
A
HOH
2015
4
HOH
HOH
2015
A
HOH
2016
4
HOH
HOH
2016
A
HOH
2017
4
HOH
HOH
2017
A
HOH
2018
4
HOH
HOH
2018
A
HOH
2019
4
HOH
HOH
2019
A
HOH
2020
4
HOH
HOH
2020
A
HOH
2021
4
HOH
HOH
2021
A
HOH
2022
4
HOH
HOH
2022
A
HOH
2023
4
HOH
HOH
2023
A
HOH
2024
4
HOH
HOH
2024
A
HOH
2025
4
HOH
HOH
2025
A
HOH
2026
4
HOH
HOH
2026
A
HOH
2028
4
HOH
HOH
2028
A
HOH
2029
4
HOH
HOH
2029
A
HOH
2030
4
HOH
HOH
2030
A
HOH
2031
4
HOH
HOH
2031
A
HOH
2032
4
HOH
HOH
2032
A
HOH
2033
4
HOH
HOH
2033
A
HOH
2034
4
HOH
HOH
2034
A
HOH
2035
4
HOH
HOH
2035
A
HOH
2036
4
HOH
HOH
2036
A
HOH
2037
4
HOH
HOH
2037
A
HOH
2038
4
HOH
HOH
2038
A
HOH
2039
4
HOH
HOH
2039
A
HOH
2040
4
HOH
HOH
2040
A
HOH
2041
4
HOH
HOH
2041
A
HOH
2042
4
HOH
HOH
2042
A
HOH
2043
4
HOH
HOH
2043
A
HOH
2044
4
HOH
HOH
2044
A
HOH
2045
4
HOH
HOH
2045
A
HOH
2046
4
HOH
HOH
2046
A
HOH
2048
4
HOH
HOH
2048
A
HOH
2049
4
HOH
HOH
2049
A
HOH
2050
4
HOH
HOH
2050
A
HOH
2051
4
HOH
HOH
2051
A
HOH
2052
4
HOH
HOH
2052
A
HOH
2053
4
HOH
HOH
2053
A
HOH
2054
4
HOH
HOH
2054
A
HOH
2055
4
HOH
HOH
2055
A
HOH
2056
4
HOH
HOH
2056
A
HOH
2057
4
HOH
HOH
2057
A
HOH
2058
4
HOH
HOH
2058
A
HOH
2059
4
HOH
HOH
2059
A
HOH
2060
4
HOH
HOH
2060
A
HOH
2061
4
HOH
HOH
2061
A
HOH
2062
4
HOH
HOH
2062
A
HOH
2063
4
HOH
HOH
2063
A
HOH
2064
4
HOH
HOH
2064
A
HOH
2001
4
HOH
HOH
2001
B
HOH
2002
4
HOH
HOH
2002
B
HOH
2003
4
HOH
HOH
2003
B
HOH
2004
4
HOH
HOH
2004
B
HOH
2005
4
HOH
HOH
2005
B
HOH
2006
4
HOH
HOH
2006
B
HOH
2007
4
HOH
HOH
2007
B
HOH
2008
4
HOH
HOH
2008
B
HOH
2009
4
HOH
HOH
2009
B
HOH
2010
4
HOH
HOH
2010
B
HOH
2011
4
HOH
HOH
2011
B
HOH
2012
4
HOH
HOH
2012
B
HOH
2013
4
HOH
HOH
2013
B
HOH
2014
4
HOH
HOH
2014
B
HOH
2015
4
HOH
HOH
2015
B
HOH
2016
4
HOH
HOH
2016
B
HOH
2017
4
HOH
HOH
2017
B
HOH
2018
4
HOH
HOH
2018
B
HOH
2019
4
HOH
HOH
2019
B
HOH
2020
4
HOH
HOH
2020
B
HOH
2021
4
HOH
HOH
2021
B
HOH
2022
4
HOH
HOH
2022
B
HOH
2023
4
HOH
HOH
2023
B
HOH
2024
4
HOH
HOH
2024
B
HOH
2025
4
HOH
HOH
2025
B
HOH
2026
4
HOH
HOH
2026
B
HOH
2027
4
HOH
HOH
2027
B
HOH
2028
4
HOH
HOH
2028
B
HOH
2029
4
HOH
HOH
2029
B
HOH
2030
4
HOH
HOH
2030
B
HOH
2031
4
HOH
HOH
2031
B
HOH
2032
4
HOH
HOH
2032
B
HOH
2033
4
HOH
HOH
2033
B
HOH
2034
4
HOH
HOH
2034
B
HOH
2035
4
HOH
HOH
2035
B
HOH
2036
4
HOH
HOH
2036
B
HOH
2037
4
HOH
HOH
2037
B
HOH
2038
4
HOH
HOH
2038
B
HOH
2039
4
HOH
HOH
2039
B
HOH
2040
4
HOH
HOH
2040
B
HOH
2042
4
HOH
HOH
2042
B
HOH
2043
4
HOH
HOH
2043
B
HOH
2044
4
HOH
HOH
2044
B
HOH
2045
4
HOH
HOH
2045
B
HOH
2047
4
HOH
HOH
2047
B
HOH
2048
4
HOH
HOH
2048
B
HOH
2049
4
HOH
HOH
2049
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
3
A
DA
4
n
4
DA
4
A
DA
5
n
5
DA
5
A
DA
6
n
6
DA
6
A
DT
7
n
7
DT
7
A
DT
8
n
8
DT
8
A
DT
9
n
9
DT
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DG
12
n
12
DG
12
A
DC
13
n
1
DC
13
B
DG
14
n
2
DG
14
B
DC
15
n
3
DC
15
B
DA
16
n
4
DA
16
B
DA
17
n
5
DA
17
B
DA
18
n
6
DA
18
B
DT
19
n
7
DT
19
B
DT
20
n
8
DT
20
B
DT
21
n
9
DT
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
24
n
12
DG
24
B
author_and_software_defined_assembly
PISA
2
dimeric
1230
-9.2
5080
A
HOH
2054
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
A
HOH
2055
E
O
HOH
1_555
89.3
A
HOH
2054
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2014
F
O
HOH
1_555
95.4
A
HOH
2055
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2014
F
O
HOH
1_555
91.7
A
HOH
2054
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2047
F
O
HOH
1_555
84.8
A
HOH
2055
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2047
F
O
HOH
1_555
85.7
B
HOH
2014
F
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2047
F
O
HOH
1_555
177.4
A
HOH
2054
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2048
F
O
HOH
1_555
88.2
A
HOH
2055
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2048
F
O
HOH
1_555
177.2
B
HOH
2014
F
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2048
F
O
HOH
1_555
89.8
B
HOH
2047
F
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2048
F
O
HOH
1_555
92.8
A
HOH
2054
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2049
F
O
HOH
1_555
172.2
A
HOH
2055
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2049
F
O
HOH
1_555
92.1
B
HOH
2014
F
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2049
F
O
HOH
1_555
92.3
B
HOH
2047
F
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2049
F
O
HOH
1_555
87.6
B
HOH
2048
F
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
B
HOH
2049
F
O
HOH
1_555
90.2
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
OP1
O
DT
HOH
8
2039
1.58
1
A
A
OP1
O
DA
HOH
5
2029
2.16
1
A
A
OP2
O
DA
HOH
4
2025
2.18
1
A
DG
2
0.063
SIDE CHAIN
1
-4.52
0.40
121.90
117.38
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
3.94
0.50
117.40
121.34
A
A
A
C4
C5
C6
DC
DC
DC
1
1
1
N
1
6.30
0.70
120.20
126.50
A
A
A
C5
C4
N4
DC
DC
DC
1
1
1
N
1
9.09
1.40
114.30
123.39
A
A
A
N9
C1'
C2'
DG
DG
DG
2
2
2
N
1
4.55
0.60
125.10
129.65
A
A
A
C6
N1
C2
DG
DG
DG
2
2
2
N
1
-3.64
0.60
123.90
120.26
A
A
A
N1
C2
N3
DG
DG
DG
2
2
2
N
1
2.60
0.40
110.80
113.40
A
A
A
C4
C5
N7
DG
DG
DG
2
2
2
N
1
-3.30
0.50
104.30
101.00
A
A
A
C5
N7
C8
DG
DG
DG
2
2
2
N
1
3.32
0.50
113.10
116.42
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
4.25
0.60
119.90
124.15
A
A
A
N1
C6
O6
DG
DG
DG
2
2
2
N
1
-4.31
0.60
128.60
124.29
A
A
A
C5
C6
O6
DG
DG
DG
2
2
2
N
1
-3.19
0.50
117.70
114.51
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
1
3.20
0.50
113.80
117.00
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
-2.64
0.40
105.80
103.16
A
A
A
C8
N9
C4
DA
DA
DA
4
4
4
N
1
5.49
0.60
118.60
124.09
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
17.40
1.50
119.60
137.00
A
A
A
OP1
P
OP2
DA
DA
DA
5
5
5
N
1
-8.13
0.90
105.70
97.57
A
A
A
O5'
P
OP2
DA
DA
DA
5
5
5
N
1
-7.67
0.70
108.00
100.33
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
-2.80
0.40
105.80
103.00
A
A
A
C8
N9
C4
DA
DA
DA
5
5
5
N
1
3.24
0.50
117.00
120.24
A
A
A
C4
C5
C6
DA
DA
DA
6
6
6
N
1
3.25
0.40
105.80
109.05
A
A
A
N9
C4
C5
DA
DA
DA
6
6
6
N
1
-5.14
0.80
105.90
100.76
A
A
A
O4'
C1'
C2'
DT
DT
DT
7
7
7
N
1
14.12
1.50
119.60
133.72
A
A
A
OP1
P
OP2
DT
DT
DT
8
8
8
N
1
4.09
0.60
119.90
123.99
A
A
A
N3
C4
O4
DT
DT
DT
9
9
9
N
1
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.79
0.50
113.10
116.89
A
A
A
N7
C8
N9
DG
DG
DG
10
10
10
N
1
6.39
0.90
116.20
122.59
A
A
A
N1
C2
N2
DG
DG
DG
10
10
10
N
1
-6.56
0.70
119.90
113.34
A
A
A
N3
C2
N2
DG
DG
DG
10
10
10
N
1
-8.30
0.70
108.00
99.70
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
8.92
1.20
119.70
128.62
A
A
A
C3'
O3'
P
DC
DC
DG
11
11
12
Y
1
-9.70
1.60
120.90
111.20
A
A
A
P
O5'
C5'
DG
DG
DG
12
12
12
N
1
-6.03
0.40
104.50
98.47
A
A
A
O4'
C4'
C3'
DG
DG
DG
12
12
12
N
1
7.93
0.90
103.10
111.03
A
A
A
C4'
C3'
C2'
DG
DG
DG
12
12
12
N
1
-4.73
0.60
123.90
119.17
A
A
A
N1
C2
N3
DG
DG
DG
12
12
12
N
1
-3.20
0.40
106.40
103.20
A
A
A
C8
N9
C4
DG
DG
DG
12
12
12
N
1
6.38
0.90
116.20
122.58
A
A
A
N1
C2
N2
DG
DG
DG
12
12
12
N
1
-5.32
0.70
108.00
102.68
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.77
0.50
119.90
123.67
B
B
B
C2
N3
C4
DC
DC
DC
13
13
13
N
1
-3.74
0.40
121.90
118.16
B
B
B
N3
C4
C5
DC
DC
DC
13
13
13
N
1
-4.34
0.60
118.90
114.56
B
B
B
N1
C2
O2
DC
DC
DC
13
13
13
N
1
4.28
0.70
121.90
126.18
B
B
B
N3
C2
O2
DC
DC
DC
15
15
15
N
1
4.79
0.70
120.20
124.99
B
B
B
C5
C4
N4
DC
DC
DC
15
15
15
N
1
3.59
0.30
108.30
111.89
B
B
B
O4'
C1'
N9
DA
DA
DA
16
16
16
N
1
4.44
0.60
118.60
123.04
B
B
B
C6
N1
C2
DA
DA
DA
16
16
16
N
1
-4.04
0.50
103.90
99.86
B
B
B
C5
N7
C8
DA
DA
DA
16
16
16
N
1
5.65
0.50
113.80
119.45
B
B
B
N7
C8
N9
DA
DA
DA
16
16
16
N
1
-3.40
0.40
105.80
102.40
B
B
B
C8
N9
C4
DA
DA
DA
16
16
16
N
1
12.53
1.50
119.60
132.13
B
B
B
OP1
P
OP2
DA
DA
DA
17
17
17
N
1
-3.70
0.40
104.50
100.80
B
B
B
O4'
C4'
C3'
DA
DA
DA
17
17
17
N
1
4.45
0.70
110.30
114.75
B
B
B
C1'
O4'
C4'
DA
DA
DA
17
17
17
N
1
3.69
0.60
106.00
109.69
B
B
B
O4'
C4'
C3'
DA
DA
DA
18
18
18
N
1
-4.71
0.70
108.00
103.29
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
3.17
0.50
129.30
132.47
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
-3.74
0.50
110.60
106.86
B
B
B
C2
N3
C4
DA
DA
DA
18
18
18
N
1
-2.63
0.40
105.80
103.17
B
B
B
C8
N9
C4
DA
DA
DA
18
18
18
N
1
-6.52
1.00
110.10
103.58
B
B
B
C1'
O4'
C4'
DT
DT
DT
19
19
19
N
1
5.26
0.70
124.90
130.16
B
B
B
C5
C4
O4
DT
DT
DT
19
19
19
N
1
15.04
1.50
119.60
134.64
B
B
B
OP1
P
OP2
DT
DT
DT
20
20
20
N
1
-6.72
0.80
109.40
102.68
B
B
B
O5'
C5'
C4'
DT
DT
DT
20
20
20
N
1
-4.98
0.60
122.90
117.92
B
B
B
C6
C5
C7
DT
DT
DT
20
20
20
N
1
-5.82
0.70
108.00
102.18
B
B
B
O4'
C1'
N1
DT
DT
DT
21
21
21
N
1
-3.01
0.40
110.80
107.79
B
B
B
C4
C5
N7
DG
DG
DG
22
22
22
N
1
11.81
1.50
119.60
131.41
B
B
B
OP1
P
OP2
DC
DC
DC
23
23
23
N
1
-10.17
0.90
105.70
95.53
B
B
B
O5'
P
OP1
DC
DC
DC
23
23
23
N
1
2.26
0.30
108.30
110.56
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
14.31
1.50
119.60
133.91
B
B
B
OP1
P
OP2
DG
DG
DG
24
24
24
N
1
-8.78
0.90
105.70
96.92
B
B
B
O5'
P
OP2
DG
DG
DG
24
24
24
N
1
4.02
0.50
106.80
110.82
B
B
B
O4'
C1'
C2'
DG
DG
DG
24
24
24
N
1
-4.41
0.60
123.90
119.49
B
B
B
N1
C2
N3
DG
DG
DG
24
24
24
N
1
A
A
O3'
C3'
DG
DG
2
2
-0.036
0.006
1.419
1.383
N
1
A
A
N3
C4
DC
DC
3
3
-0.047
0.007
1.335
1.288
N
1
A
A
N9
C4
DA
DA
4
4
0.040
0.006
1.374
1.414
N
1
A
A
O3'
C3'
DT
DT
7
7
-0.082
0.006
1.419
1.337
N
1
A
A
C2
O2
DT
DT
7
7
-0.061
0.008
1.220
1.159
N
1
A
A
P
OP2
DT
DT
8
8
-0.120
0.017
1.485
1.365
N
1
A
A
O3'
C3'
DT
DT
8
8
-0.095
0.006
1.419
1.324
N
1
A
A
C5
C6
DT
DT
8
8
-0.046
0.007
1.339
1.293
N
1
A
A
C2
O2
DT
DT
8
8
-0.079
0.008
1.220
1.141
N
1
A
A
C4
O4
DT
DT
8
8
-0.069
0.009
1.228
1.159
N
1
A
A
P
OP1
DT
DT
9
9
-0.112
0.017
1.485
1.373
N
1
A
A
P
OP2
DT
DT
9
9
-0.142
0.017
1.485
1.343
N
1
A
A
C6
N1
DT
DT
9
9
-0.043
0.007
1.378
1.335
N
1
A
A
C2
O2
DT
DT
9
9
-0.057
0.008
1.220
1.163
N
1
A
A
C4
O4
DT
DT
9
9
-0.061
0.009
1.228
1.167
N
1
A
A
N3
C4
DC
DC
11
11
0.048
0.007
1.335
1.383
N
1
A
A
C2
N3
DG
DG
12
12
0.062
0.008
1.323
1.385
N
1
A
A
C5
N7
DG
DG
12
12
-0.037
0.006
1.388
1.351
N
1
B
B
P
O5'
DA
DA
16
16
-0.068
0.010
1.593
1.525
N
1
B
B
O3'
C3'
DA
DA
16
16
-0.044
0.006
1.419
1.375
N
1
B
B
P
O5'
DA
DA
17
17
0.060
0.010
1.593
1.653
N
1
B
B
O3'
C3'
DA
DA
17
17
-0.084
0.006
1.419
1.335
N
1
B
B
P
OP2
DT
DT
21
21
-0.112
0.017
1.485
1.373
N
1
B
B
C4
O4
DT
DT
21
21
-0.066
0.009
1.228
1.162
N
1
B
B
O3'
C3'
DG
DG
22
22
-0.093
0.006
1.419
1.326
N
1
B
B
N1
C2
DG
DG
22
22
-0.050
0.008
1.373
1.323
N
1
B
B
C8
N9
DG
DG
22
22
-0.044
0.007
1.374
1.330
N
1
B
B
O3'
P
DG
DC
22
23
-0.074
0.012
1.607
1.533
Y
1
B
B
C2
O2
DC
DC
23
23
-0.060
0.009
1.240
1.180
N
1
B
B
N1
C6
DC
DC
23
23
-0.037
0.006
1.367
1.330
N
1
B
B
C2
N3
DC
DC
23
23
-0.052
0.008
1.353
1.301
N
1
B
B
N3
C4
DC
DC
23
23
-0.055
0.007
1.335
1.280
N
1
B
B
C5
C6
DC
DC
23
23
-0.053
0.008
1.339
1.286
N
16.275
-0.02
0.00
0.00
-0.05
0.00
0.07
0.972
0.949
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
0.25036
0.18410
0.18718
1.42
33.04
520
10451
4.7
95.88
1.641
0.064
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.076
0.090
0.80
0.80
1.40
PDB ENTRY 1S2R
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.42
33.04
109
623
28
486
0
0.025
0.021
574
0.014
0.020
238
3.408
2.986
879
1.448
3.030
579
0.142
0.200
94
0.031
0.020
287
0.001
0.021
57
2.381
3.000
574
3.283
4.500
879
0.359
0.272
1.457
37
784
20
98.80
0
1.42
38.88
4AH1
11003
0.0
0.05
1
13.80
4.40
96.6
0.47
1.42
1.50
2.80
1
4.4
98.2
refinement
REFMAC
5.5.0110
data reduction
MOSFLM
data scaling
SCALA
phasing
PHASER
CRYSTAL STRUCTURE OF THE DB 921-D(CGCAAATTTGCG)2 COMPLEX AT 1.42 A RESOLUTION
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
metalc
2.075
A
HOH
2054
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
metalc
2.074
A
HOH
2055
E
O
HOH
1_555
B
MG
2000
D
MG
MG
1_555
metalc
1.995
B
MG
2000
D
MG
MG
1_555
B
HOH
2014
F
O
HOH
1_555
metalc
2.172
B
MG
2000
D
MG
MG
1_555
B
HOH
2047
F
O
HOH
1_555
metalc
2.117
B
MG
2000
D
MG
MG
1_555
B
HOH
2048
F
O
HOH
1_555
metalc
2.082
B
MG
2000
D
MG
MG
1_555
B
HOH
2049
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
21
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
21
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
19
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
19
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
16
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
16
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
DNA, DNA DOUBLE HELIX, MINOR GROOVE, DODECAMER, A3T3, DNA-DRUG COMPLEX, DNA HYDRATION
4AH1
PDB
1
4AH1
1
12
4AH1
1
12
4AH1
A
1
1
12
13
24
4AH1
13
24
4AH1
B
1
1
12
BINDING SITE FOR RESIDUE D2A A 1013
A
D2A
1013
Software
13
BINDING SITE FOR RESIDUE MG B 2000
B
MG
2000
Software
6
A
DA
6
A
DA
6
13
1_555
A
DT
7
A
DT
7
13
1_555
A
DT
8
A
DT
8
13
1_555
A
DT
9
A
DT
9
13
1_555
A
HOH
2035
E
HOH
13
4_455
A
HOH
2046
E
HOH
13
1_555
A
HOH
2062
E
HOH
13
1_555
A
HOH
2063
E
HOH
13
1_555
B
DA
18
B
DA
6
13
1_555
B
DT
19
B
DT
7
13
1_555
B
DT
20
B
DT
8
13
1_555
B
DT
21
B
DT
9
13
1_555
B
DG
22
B
DG
10
13
1_555
A
HOH
2054
E
HOH
6
1_555
A
HOH
2055
E
HOH
6
1_555
B
HOH
2014
F
HOH
6
1_555
B
HOH
2047
F
HOH
6
1_555
B
HOH
2048
F
HOH
6
1_555
B
HOH
2049
F
HOH
6
1_555
19
P 21 21 21