0.026624
0.015370
0.000000
0.000000
0.030742
0.000000
0.000000
0.000000
0.015293
0.00000
0.00000
0.00000
Cruse, W.B.T.
Shepard, W.
Prange, T.
delalFortelle, E.
Fourme, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
37.560
37.560
65.390
C9 H13 Br N3 O7 P
386.093
n
5-BROMO-2'-DEOXY-CYTIDINE-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
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
non-polymer
N
1
N
BR
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
N
N
13
N
C
N
14
N
C
N
15
N
C
N
16
R
C
N
17
N
O
N
18
R
C
N
19
S
C
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
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
Y
51
N
C
N
52
N
N
Y
53
N
N
Y
54
N
C
Y
55
N
N
Y
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
N
83
N
N
N
84
N
C
N
85
N
O
N
86
N
N
N
87
N
C
N
88
N
N
N
89
N
C
N
90
N
C
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
H
N
105
N
O
N
106
N
P
N
107
N
O
N
108
N
O
N
109
N
O
N
110
N
C
N
111
R
C
N
112
N
O
N
113
S
C
N
114
N
O
N
115
N
C
N
116
R
C
Y
117
N
N
Y
118
N
C
Y
119
N
N
Y
120
N
C
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
N
N
126
N
N
Y
127
N
C
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
H
N
142
N
O
N
143
N
P
N
144
N
O
N
145
N
O
N
146
N
O
N
147
N
C
N
148
R
C
N
149
N
O
N
150
S
C
N
151
N
O
N
152
N
C
N
153
R
C
N
154
N
N
N
155
N
C
N
156
N
O
N
157
N
N
N
158
N
C
N
159
N
O
N
160
N
C
N
161
N
C
N
162
N
C
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
O
N
179
N
H
N
180
N
H
N
181
N
CO
N
182
N
N
N
183
N
N
N
184
N
N
N
185
N
N
N
186
N
N
N
187
N
N
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
1
N
sing
N
2
N
doub
N
3
N
sing
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
doub
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
doub
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
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
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
N
58
N
sing
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
Y
64
N
sing
Y
65
N
doub
N
66
N
sing
Y
67
N
doub
N
68
N
sing
N
69
N
sing
Y
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
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
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
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
N
131
N
sing
Y
132
N
sing
Y
133
N
sing
Y
134
N
doub
N
135
N
sing
Y
136
N
sing
N
137
N
sing
Y
138
N
doub
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
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
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
doub
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
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
UK
Structure
STRUE6
2005
0969-2126
6
849
861
10.1016/S0969-2126(98)00087-2
9687367
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
1998
US
Science
SCIEAS
0038
0036-8075
273
1696
1699
RNA Tertiary Structure Mediation by Adenosine Platforms
1997
UK
Structure
STRUE6
2005
0969-2126
5
713
721
Solution Structure of a Metal-binding Site in the Major Groove of RNA Complexed with Cobalt(III) Hexammine
1997
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
17
2223
2231
Extraordinary Stable Structure of Short Single-Stranded DNA Fragments Containing a Specific Base Sequence: d(GCGAAAGC)
1989
US
Biochemistry
BICHAW
0033
0006-2960
24
237
240
Structural Basis for Stabilisation of Z-DNA by Cobalt Haxaammine and Magnesium Cations
1985
10.2210/pdb376d/pdb
pdb_0000376d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
276.00
1
DOUBLE MONO + MULTILAYER FOCUS
IMAGE PLATE
1996-09-01
MARRESEARCH
SI(III)
MAD
M
x-ray
1
1.0
DW21B
LURE
SYNCHROTRON
LURE BEAMLINE DW21B
2843.733
DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')
1
man
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
18.015
water
18
nat
water
no
yes
(DG)(CBR)(DG)(DA)(DA)(DA)(DG)(DC)(DT)
GCGAAAGCT
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
3
2.30
36.0000
WATER
1
CACODYLATE
1
[CO(NH3)6]3+
1
MPD
1
-1.257
1
19
A
1
A
8
1.074
A_DG1:DC8_A
1
6.292
-0.647
-0.222
-0.153
9.376
1
19
A
2
A
7
-1.394
A_CBR2:DG7_A
2
8.175
0.219
-0.208
-0.072
25.035
9
11
A
3
A
6
9.917
A_DG3:DA6_A
3
-14.740
6.327
1.417
-4.151
-1.257
1
19
A
1
A
8
1.074
A_DG1:DC8_A
4
6.292
-0.647
-0.222
-0.153
9.376
1
19
A
2
A
7
-1.394
A_CBR2:DG7_A
5
8.175
0.219
-0.208
-0.072
25.035
9
11
A
3
A
6
9.917
A_DG3:DA6_A
6
-14.740
6.327
1.417
-4.151
3.164
31.068
A
A
1
2
1.767
A
A
8
7
3.177
0.946
0.234
0.042
AA_DG1CBR2:DG7DC8_AA
1
-1.360
2.540
31.025
-0.097
-0.690
3.403
52.230
A
A
2
3
9.837
A
A
7
6
3.201
8.626
0.476
1.572
AA_CBR2DG3:DA6DG7_AA
2
-0.143
0.163
51.562
1.206
-0.550
3.164
31.068
A
A
1
2
1.767
A
A
8
7
3.177
0.946
0.234
0.042
AA_DG1CBR2:DG7DC8_AA
3
-1.360
2.540
31.025
-0.097
-0.690
3.403
52.230
A
A
2
3
9.837
A
A
7
6
3.201
8.626
0.476
1.572
AA_CBR2DG3:DA6DG7_AA
4
-0.143
0.163
51.562
1.206
-0.550
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1999-10-26
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
NDB
Y
NDB
1998-01-22
REL
NCO
COBALT HEXAMMINE(III)
HOH
water
NCO
10
2
NCO
NCO
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
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
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
G
1
n
1
DG
1
A
BRO
2
n
2
CBR
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
A
6
n
6
DA
6
A
G
7
n
7
DG
7
A
C
8
n
8
DC
8
A
T
9
n
9
DT
9
A
author_defined_assembly
2
dimeric
A
CBR
2
A
CBR
2
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
0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
10_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
18.7800000000
32.5279141661
32.6950000000
1
A
NCO
10
B
NCO
1
A
N3
NCO
10
B
N3
NCO
1
1
N
1
A
N4
NCO
10
B
N4
NCO
1
1
N
1
A
N5
NCO
10
B
N5
NCO
1
1
N
1
A
N6
NCO
10
B
N6
NCO
1
1
N
1
3.68
0.30
108.30
111.98
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
-4.23
0.60
125.10
120.87
A
A
A
C6
N1
C2
DG
DG
DG
1
1
1
N
1
4.06
0.60
123.90
127.96
A
A
A
N1
C2
N3
DG
DG
DG
1
1
1
N
1
2.60
0.40
105.40
108.00
A
A
A
N9
C4
C5
DG
DG
DG
1
1
1
N
1
-4.73
0.60
119.90
115.17
A
A
A
N1
C6
O6
DG
DG
DG
1
1
1
N
1
9.92
1.20
119.70
129.62
A
A
A
C3'
O3'
P
DG
DG
CBR
1
1
2
Y
1
-7.83
0.80
102.40
94.57
A
A
A
C3'
C2'
C1'
DG
DG
DG
3
3
3
N
1
8.83
0.30
108.30
117.13
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-4.97
0.60
128.60
123.63
A
A
A
C5
C6
O6
DG
DG
DG
3
3
3
N
1
-3.73
0.50
129.30
125.57
A
A
A
N1
C2
N3
DA
DA
DA
4
4
4
N
1
3.23
0.30
108.30
111.53
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
-3.12
0.50
129.30
126.18
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
-4.37
0.50
129.30
124.93
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
5.73
0.30
108.30
114.03
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
3.55
0.30
108.30
111.85
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
-4.96
0.60
127.20
122.24
A
A
A
C2
N3
C4
DT
DT
DT
9
9
9
N
1
4.39
0.60
115.20
119.59
A
A
A
N3
C4
C5
DT
DT
DT
9
9
9
N
1
A
A
C4
O4
DT
DT
9
9
0.108
0.009
1.228
1.336
N
0.241
0.189
0.189
2.100
15.000
183
1832
10.000
95.000
1
MAD AT BROMINE EDGE
MANUALLY BUILT IN THE EXPERIMENTAL DENSITY
0.15
15.0
2.100
15.000
18
206
4
184
0
0.012
0.023
2.30
2.100
15.000
376D
1832
3.000
0.053
1
11.3000
95.000
0.148
2.100
4.200
61.00
model building
MADLSQ
+ CCP4 PACKAGE
refinement
X-PLOR
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
phasing
MADLSQ
phasing
CCP4
A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)
1
N
N
2
N
N
3
N
N
covale
1.602
both
A
DG
1
A
O3'
DG
1
1_555
A
CBR
2
A
P
CBR
2
1_555
covale
1.612
both
A
CBR
2
A
O3'
CBR
2
1_555
A
DG
3
A
P
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
8
A
N3
DC
8
8_665
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
8
A
O2
DC
8
8_665
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
8_665
hydrog
WATSON-CRICK
A
CBR
2
A
N3
CBR
2
1_555
A
DG
7
A
N1
DG
7
8_665
hydrog
WATSON-CRICK
A
CBR
2
A
N4
CBR
2
1_555
A
DG
7
A
O6
DG
7
8_665
hydrog
WATSON-CRICK
A
CBR
2
A
O2
CBR
2
1_555
A
DG
7
A
N2
DG
7
8_665
hydrog
TYPE_11_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DA
6
A
N7
DA
6
8_665
hydrog
TYPE_11_PAIR
A
DG
3
A
N3
DG
3
1_555
A
DA
6
A
N6
DA
6
8_665
hydrog
TYPE_11_PAIR
A
DA
6
A
N6
DA
6
1_555
A
DG
3
A
N3
DG
3
8_665
hydrog
TYPE_11_PAIR
A
DA
6
A
N7
DA
6
1_555
A
DG
3
A
N2
DG
3
8_665
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
A
CBR
2
A
N3
CBR
2
8_665
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
A
CBR
2
A
O2
CBR
2
8_665
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
A
CBR
2
A
N4
CBR
2
8_665
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
A
DG
1
A
N1
DG
1
8_665
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
8_665
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
A
DG
1
A
N2
DG
1
8_665
DNA
RIGHT HANDED DNA, DOUBLE HELIX, OVERHANGING BASE, MODIFIED, MISMATCHED, DNA
376D
PDB
1
376D
1
9
376D
1
9
376D
A
1
1
9
BINDING SITE FOR RESIDUE NCO A 10
A
NCO
10
Software
5
A
CBR
2
A
CBR
2
5
2_655
A
DG
3
A
DG
3
5
1_555
A
DG
3
A
DG
3
5
2_655
A
HOH
14
C
HOH
5
1_555
A
HOH
23
C
HOH
5
2_655
182
hexagonal
P 63 2 2