0.022573
0.000000
0.000000
0.000000
0.022573
0.000000
0.000000
0.000000
0.040323
0.00000
0.00000
0.00000
Ramakrishnan, B.
Sekharudu, C.
Pan, B.C.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.0
90.0
90.0
44.3
44.3
24.8
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
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
CO
N
148
N
N
N
149
N
N
N
150
N
N
N
151
N
N
N
152
N
N
N
153
N
N
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
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
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
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
59
67
72
10.1107/S0907444902018917
12499541
Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA.
2003
10.2210/pdb1m77/pdb
pdb_00001m77
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
mirrors
AREA DETECTOR
1993-09-22
NICOLET
graphite
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
SIEMENS
3045.992
5'-D(*CP*CP*CP*GP*AP*TP*CP*GP*GP*G)-3'
1
syn
polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
18.015
water
34
nat
water
no
no
(DC)(DC)(DC)(DG)(DA)(DT)(DC)(DG)(DG)(DG)
CCCGATCGGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
1.91
35.50
VAPOR DIFFUSION, HANGING DROP
6.0
cobalt hexammine, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
cobalt hexammine
1
cacodylate
1
1.441
1
19
A
1
A
10
0.027
A_DC1:DG10_A
1
-9.247
0.086
0.092
-0.093
7.020
1
19
A
2
A
9
-2.022
A_DC2:DG9_A
2
-17.995
0.182
-0.032
-0.230
-0.469
1
19
A
3
A
8
1.890
A_DC3:DG8_A
3
-17.396
0.258
0.135
-0.173
-17.409
1
19
A
4
A
7
-0.368
A_DG4:DC7_A
4
-11.261
-0.174
-0.354
-0.119
-7.473
1
20
A
5
A
6
0.517
A_DA5:DT6_A
5
-8.842
0.099
0.063
-0.151
7.473
1
20
A
6
A
5
0.517
A_DT6:DA5_A
6
-8.842
-0.099
0.063
-0.151
17.409
1
19
A
7
A
4
-0.368
A_DC7:DG4_A
7
-11.261
0.174
-0.354
-0.119
0.469
1
19
A
8
A
3
1.890
A_DG8:DC3_A
8
-17.396
-0.258
0.135
-0.173
-7.019
1
19
A
9
A
2
-2.022
A_DG9:DC2_A
9
-17.995
-0.182
-0.032
-0.230
-1.441
1
19
A
10
A
1
0.027
A_DG10:DC1_A
10
-9.247
-0.086
0.092
-0.093
3.079
37.624
A
A
1
2
4.749
A
A
10
9
3.166
3.058
-0.349
-1.153
AA_DC1DC2:DG9DG10_AA
1
-1.912
2.969
37.457
-2.167
0.303
3.257
32.100
A
A
2
3
8.574
A
A
9
8
3.543
4.722
0.486
-1.494
AA_DC2DC3:DG8DG9_AA
2
-1.981
3.596
31.700
-3.589
-1.251
2.413
37.664
A
A
3
4
29.539
A
A
8
7
3.639
18.312
-0.889
-1.626
AA_DC3DG4:DC7DG8_AA
3
1.032
-1.664
33.039
-4.875
1.510
1.856
27.852
A
A
4
5
30.701
A
A
7
6
3.121
14.115
0.972
-1.665
AA_DG4DA5:DT6DC7_AA
4
-0.480
1.045
24.067
-6.225
-2.114
2.950
30.375
A
A
5
6
7.885
A
A
6
5
3.175
4.119
0.000
-1.486
AA_DA5DT6:DA5DT6_AA
5
0.000
0.000
30.101
-3.613
0.000
1.856
27.852
A
A
6
7
30.701
A
A
5
4
3.121
14.115
-0.972
-1.665
AA_DT6DC7:DG4DA5_AA
6
0.480
-1.045
24.067
-6.225
2.114
2.413
37.664
A
A
7
8
29.539
A
A
4
3
3.639
18.312
0.889
-1.626
AA_DC7DG8:DC3DG4_AA
7
-1.032
1.664
33.039
-4.875
-1.510
3.257
32.100
A
A
8
9
8.574
A
A
3
2
3.543
4.722
-0.486
-1.494
AA_DG8DG9:DC2DC3_AA
8
1.981
-3.596
31.700
-3.589
1.251
3.079
37.624
A
A
9
10
4.749
A
A
2
1
3.166
3.058
0.349
-1.153
AA_DG9DG10:DC1DC2_AA
9
1.912
-2.969
37.457
-2.167
-0.303
software
chem_comp_atom
chem_comp_bond
database_2
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-01-07
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-10-11
1
4
2024-02-14
1
5
2024-04-03
_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
RCSB
2002-07-18
REL
REL
NCO
COBALT HEXAMMINE(III)
HOH
water
fiber A-DNA
Other
experimental model
COH
201
2
NCO
NCO
201
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
HOH
125
3
HOH
HOH
125
A
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
128
3
HOH
HOH
128
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
132
3
HOH
HOH
132
A
HOH
133
3
HOH
HOH
133
A
HOH
134
3
HOH
HOH
134
A
CYT
1
n
1
DC
1
A
CYT
2
n
2
DC
2
A
CYT
3
n
3
DC
3
A
GUA
4
n
4
DG
4
A
ADE
5
n
5
DA
5
A
THY
6
n
6
DT
6
A
CYT
7
n
7
DC
7
A
GUA
8
n
8
DG
8
A
GUA
9
n
9
DG
9
A
GUA
10
n
10
DG
10
A
author_defined_assembly
2
dimeric
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
DC
1
0.076
SIDE CHAIN
1
A
DC
2
0.112
SIDE CHAIN
1
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
4.59
0.30
108.30
112.89
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
7.13
1.10
110.50
117.63
A
A
A
O3'
P
OP2
DA
DT
DT
5
6
6
Y
1
-3.76
0.60
122.90
119.14
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
9.54
1.10
110.50
120.04
A
A
A
O3'
P
OP2
DT
DC
DC
6
7
7
Y
1
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
4.13
0.30
108.30
112.43
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
0.185
0.163
1.25
8.0
653
5969
5316
random
1
isotropic
2
MOLECULAR REPLACEMENT
fiber A-DNA
1.25
8.0
34
243
7
202
0
0.224
0.197
1.31
52
1.25
28.0
1M77
7785
6929
1.0
1.0
0.055
1
7.4
90
1.25
1.31
433
data scaling
X-GEN
2.0
data reduction
X-GEN
2.0
refinement
X-PLOR
Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
10
A
N1
DG
10
7_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
10
A
O6
DG
10
7_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
10
A
N2
DG
10
7_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
9
A
N1
DG
9
7_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
9
A
O6
DG
9
7_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
9
A
N2
DG
9
7_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
A
DG
8
A
N1
DG
8
7_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
A
DG
8
A
O6
DG
8
7_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
A
DG
8
A
N2
DG
8
7_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
7
A
N3
DC
7
7_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
7
A
O2
DC
7
7_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
7
A
N4
DC
7
7_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
A
DT
6
A
N3
DT
6
7_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
A
DT
6
A
O4
DT
6
7_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
A
DA
5
A
N1
DA
5
7_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
A
DA
5
A
N6
DA
5
7_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
A
DG
4
A
N1
DG
4
7_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
A
DG
4
A
O6
DG
4
7_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
A
DG
4
A
N2
DG
4
7_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
A
DC
3
A
N3
DC
3
7_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
A
DC
3
A
O2
DC
3
7_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
A
DC
3
A
N4
DC
3
7_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
A
DC
2
A
N3
DC
2
7_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
A
DC
2
A
O2
DC
2
7_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
A
DC
2
A
N4
DC
2
7_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
A
DC
1
A
N3
DC
1
7_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
A
DC
1
A
O2
DC
1
7_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
A
DC
1
A
N4
DC
1
7_555
DNA
A-DNA, Cobalt hexammine, DNA
1M77
PDB
1
1M77
1
10
1M77
1
10
1M77
A
1
1
10
BINDING SITE FOR RESIDUE NCO A 201
A
NCO
201
Software
12
A
DC
3
A
DC
3
12
5_545
A
DG
4
A
DG
4
12
5_545
A
DA
5
A
DA
5
12
7_556
A
DG
9
A
DG
9
12
4_555
A
DG
9
A
DG
9
12
1_555
A
DG
10
A
DG
10
12
4_555
A
HOH
101
C
HOH
12
1_555
A
HOH
102
C
HOH
12
1_555
A
HOH
103
C
HOH
12
1_555
A
HOH
104
C
HOH
12
7_556
A
HOH
111
C
HOH
12
5_545
A
HOH
123
C
HOH
12
7_556
96
P 43 21 2