0.023635
0.000000
0.000000
0.000000
0.023635
0.000000
0.000000
0.000000
0.041135
0.00000
0.00000
0.00000
Zhang, W.
Coronado, G.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
42.310
42.310
24.310
C11 H17 N2 O8 P Se
415.195
n
5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
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
Pt 2
195.078
PLATINUM (II) 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
N
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
O
N
13
N
C
N
14
N
C
N
15
R
C
N
16
N
C
N
17
R
C
N
18
N
O
N
19
R
C
N
20
R
C
N
21
N
SE
N
22
N
C
N
23
N
O
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
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
O
N
42
N
P
N
43
N
O
N
44
N
O
N
45
N
O
N
46
N
C
N
47
R
C
N
48
N
O
N
49
S
C
N
50
N
O
N
51
N
C
N
52
R
C
Y
53
N
N
Y
54
N
C
Y
55
N
N
Y
56
N
C
Y
57
N
C
N
58
N
N
Y
59
N
N
Y
60
N
C
Y
61
N
N
Y
62
N
C
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
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
O
N
78
N
P
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
O
N
85
S
C
N
86
N
O
N
87
N
C
N
88
R
C
N
89
N
N
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
C
N
96
N
C
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
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
N
C
N
122
R
C
Y
123
N
N
Y
124
N
C
Y
125
N
N
Y
126
N
C
N
127
N
C
N
128
N
O
N
129
N
N
N
130
N
C
N
131
N
N
N
132
N
N
Y
133
N
C
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
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
PT
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
doub
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
doub
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
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
doub
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
sing
Y
65
N
sing
Y
66
N
sing
Y
67
N
doub
N
68
N
sing
Y
69
N
sing
Y
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
73
N
doub
N
74
N
sing
N
75
N
sing
Y
76
N
sing
Y
77
N
doub
N
78
N
sing
Y
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
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
sing
N
100
N
sing
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
doub
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
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
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
Y
138
N
sing
Y
139
N
sing
Y
140
N
doub
N
141
N
sing
Y
142
N
sing
N
143
N
sing
Y
144
N
doub
N
145
N
doub
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
To be Published
0353
DNA octamer D (GTseGTACAC) partially crosslinked with platinum
10.2210/pdb4h5a/pdb
pdb_00004h5a
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
99
1
CCD
2012-07-13
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
8.2.2
ALS
0.9795
SYNCHROTRON
ALS BEAMLINE 8.2.2
short DNA 8mer with Se modification
2520.592
DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3')
1
syn
polymer
195.078
PLATINUM (II) ION
1
syn
non-polymer
18.015
water
36
nat
water
no
yes
(DG)(2ST)(DG)(DG)(DC)(DC)(DA)(DC)
GTGGCCAC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
5
2.16
43.01
VAPOR DIFFUSION, HANGING DROP
6.8
the platinum was added to the crystallization buffer , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
-20.786
1
19
A
1
A
8
1.784
A_DG1:DC8_A
1
-9.164
-0.381
-0.355
-0.011
-7.576
1
20
A
2
A
7
-1.021
A_2ST2:DA7_A
2
-12.387
-0.169
0.126
-0.105
-5.038
1
19
A
3
A
6
-1.523
A_DG3:DC6_A
3
-11.692
-0.220
0.134
-0.218
-5.367
1
19
A
4
A
5
-0.746
A_DG4:DC5_A
4
-14.376
-0.176
0.099
-0.079
5.367
1
19
A
5
A
4
-0.746
A_DC5:DG4_A
5
-14.375
0.176
0.099
-0.079
5.038
1
19
A
6
A
3
-1.523
A_DC6:DG3_A
6
-11.692
0.220
0.134
-0.218
7.576
1
20
A
7
A
2
-1.021
A_DA7:2ST2_A
7
-12.387
0.169
0.126
-0.105
20.786
1
19
A
8
A
1
1.784
A_DC8:DG1_A
8
-9.164
0.381
-0.355
-0.011
2.660
32.592
A
A
1
2
16.935
A
A
8
7
3.074
9.366
-0.047
-1.014
AA_DG12ST2:DA7DC8_AA
1
-2.722
4.922
31.136
-3.270
-0.342
2.619
30.493
A
A
2
3
17.549
A
A
7
6
3.143
9.093
0.599
-1.409
AA_2ST2DG3:DC6DA7_AA
2
1.423
-2.747
29.102
-4.314
-0.883
2.928
35.859
A
A
3
4
9.713
A
A
6
5
3.224
5.948
0.375
-1.701
AA_DG3DG4:DC5DC6_AA
3
2.924
-4.774
35.261
-3.572
-0.211
2.914
29.538
A
A
4
5
9.034
A
A
5
4
3.111
4.588
0.000
-1.061
AA_DG4DC5:DG4DC5_AA
4
0.000
0.000
29.187
-2.984
0.000
2.928
35.859
A
A
5
6
9.713
A
A
4
3
3.224
5.948
-0.375
-1.701
AA_DC5DC6:DG3DG4_AA
5
-2.924
4.774
35.261
-3.572
0.211
2.619
30.493
A
A
6
7
17.549
A
A
3
2
3.143
9.093
-0.599
-1.409
AA_DC6DA7:2ST2DG3_AA
6
-1.423
2.747
29.102
-4.314
0.883
2.660
32.592
A
A
7
8
16.935
A
A
2
1
3.074
9.366
0.047
-1.014
AA_DA7DC8:DG12ST2_AA
7
2.722
-4.922
31.136
-3.270
0.342
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
1
0
2012-10-03
1
1
2024-02-28
_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
Se-DNA without platinum crosslinked
RCSB
Y
RCSB
2012-09-18
REL
REL
PT
PLATINUM (II) ION
HOH
water
PT
1
2
PT
PT
101
A
HOH
1
3
HOH
HOH
201
A
HOH
2
3
HOH
HOH
202
A
HOH
3
3
HOH
HOH
203
A
HOH
4
3
HOH
HOH
204
A
HOH
5
3
HOH
HOH
205
A
HOH
6
3
HOH
HOH
206
A
HOH
7
3
HOH
HOH
207
A
HOH
8
3
HOH
HOH
208
A
HOH
10
3
HOH
HOH
209
A
HOH
11
3
HOH
HOH
210
A
HOH
14
3
HOH
HOH
211
A
HOH
18
3
HOH
HOH
212
A
HOH
19
3
HOH
HOH
213
A
HOH
20
3
HOH
HOH
214
A
HOH
21
3
HOH
HOH
215
A
HOH
22
3
HOH
HOH
216
A
HOH
23
3
HOH
HOH
217
A
HOH
24
3
HOH
HOH
218
A
HOH
25
3
HOH
HOH
219
A
HOH
26
3
HOH
HOH
220
A
HOH
27
3
HOH
HOH
221
A
HOH
28
3
HOH
HOH
222
A
HOH
29
3
HOH
HOH
223
A
HOH
32
3
HOH
HOH
224
A
HOH
33
3
HOH
HOH
225
A
HOH
35
3
HOH
HOH
226
A
HOH
36
3
HOH
HOH
227
A
HOH
37
3
HOH
HOH
228
A
HOH
39
3
HOH
HOH
229
A
HOH
41
3
HOH
HOH
230
A
HOH
46
3
HOH
HOH
231
A
HOH
47
3
HOH
HOH
232
A
HOH
48
3
HOH
HOH
233
A
HOH
49
3
HOH
HOH
234
A
HOH
50
3
HOH
HOH
235
A
HOH
51
3
HOH
HOH
236
A
G
1
n
1
DG
1
A
2ST
2
n
2
2ST
2
A
G
3
n
3
DG
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
C
6
n
6
DC
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
author_and_software_defined_assembly
PISA
2
dimeric
2210
-30
2880
A
2ST
2
A
2ST
2
DT
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
8_554
-y,-x,-z-1/2
crystal symmetry operation
0.0000000000
0.0000000000
-12.1550000000
1
A
HOH
234
C
HOH
1
A
A
O
O
HOH
HOH
209
223
1.79
1
A
A
OP2
O
DG
HOH
3
231
1.94
1
A
A
O
O
HOH
HOH
222
223
2.00
1
A
A
O
O
HOH
HOH
227
231
2.11
1
A
A
O3'
P
2ST
DG
2
3
1.77
1
7.36
1.20
115.70
123.06
A
A
A
C5'
C4'
C3'
DG
DG
DG
3
3
3
N
1
-10.33
0.70
102.20
91.87
A
A
A
C4'
C3'
C2'
DG
DG
DG
3
3
3
N
1
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
5.42
0.50
128.60
134.02
A
A
A
N3
C4
C5
DG
DG
DG
3
3
3
N
1
-4.13
0.50
104.30
100.17
A
A
A
C5
N7
C8
DG
DG
DG
3
3
3
N
1
4.68
0.50
113.10
117.78
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-4.15
0.60
126.00
121.85
A
A
A
N3
C4
N9
DG
DG
DG
3
3
3
N
1
-4.23
0.40
104.50
100.27
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
-4.86
0.70
121.90
117.04
A
A
A
N3
C2
O2
DC
DC
DC
5
5
5
N
1
-2.40
0.40
104.50
102.10
A
A
A
O4'
C4'
C3'
DC
DC
DC
6
6
6
N
1
-2.55
0.40
121.90
119.35
A
A
A
N3
C4
C5
DC
DC
DC
6
6
6
N
1
5.17
0.70
121.90
127.07
A
A
A
N3
C2
O2
DC
DC
DC
6
6
6
N
1
-2.94
0.40
104.50
101.56
A
A
A
O4'
C4'
C3'
DA
DA
DA
7
7
7
N
1
4.18
0.60
118.60
122.78
A
A
A
C6
N1
C2
DA
DA
DA
7
7
7
N
1
-3.95
0.50
129.30
125.35
A
A
A
N1
C2
N3
DA
DA
DA
7
7
7
N
1
-2.73
0.40
105.80
103.07
A
A
A
N9
C4
C5
DA
DA
DA
7
7
7
N
1
4.42
0.60
118.60
123.02
A
A
A
N1
C6
N6
DA
DA
DA
7
7
7
N
1
5.83
0.90
103.10
108.93
A
A
A
C4'
C3'
C2'
DC
DC
DC
8
8
8
N
1
-6.68
0.70
119.20
112.52
A
A
A
N1
C2
N3
DC
DC
DC
8
8
8
N
1
5.47
0.50
119.90
125.37
A
A
A
C2
N3
C4
DC
DC
DC
8
8
8
N
1
4.28
0.70
121.90
126.18
A
A
A
N3
C2
O2
DC
DC
DC
8
8
8
N
1
A
A
O3'
P
2ST
DG
2
3
0.160
0.012
1.607
1.767
Y
1
A
A
C5
N7
DG
DG
3
3
0.044
0.006
1.388
1.432
N
1
A
A
N3
C4
DC
DC
8
8
-0.043
0.007
1.335
1.292
N
1
A
A
O
O
HOH
HOH
224
232
1.98
1_555
7_655
19.524
-0.02
0.00
0.00
-0.02
0.00
0.03
0.956
0.940
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.23708
0.21187
0.21317
1.42
21.08
206
4265
4.6
99.25
1.458
0.057
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.074
0.074
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
1.42
21.08
36
200
1
163
0
0.027
0.021
180
3.145
3.000
271
0.437
0.200
32
0.029
0.020
84
2.456
3.000
180
3.151
4.500
271
0.457
0.402
1.455
20
293
20
96.01
1.42
21.08
4H5A
4265
0.091
1
17.93
12.5
0.584
1.42
1.47
3.73
1
9.5
99.5
data collection
HKL-2000
phasing
PHASES
refinement
REFMAC
5.5.0110
data reduction
HKL-2000
data scaling
HKL-2000
DNA octamer D (GTseGTACAC) partially crosslinked with platinum
1
N
N
2
N
N
3
N
N
covale
1.625
both
A
DG
1
A
O3'
DG
1
1_555
A
2ST
2
A
P
2ST
2
1_555
covale
1.767
both
A
2ST
2
A
O3'
2ST
2
1_555
A
DG
3
A
P
DG
3
1_555
metalc
2.175
A
DG
4
A
N7
DG
4
1_555
A
PT
101
B
PT
PT
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
8
A
N3
DC
8
8_554
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
8
A
O2
DC
8
8_554
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
8_554
hydrog
WATSON-CRICK
A
2ST
2
A
N3
2ST
2
1_555
A
DA
7
A
N1
DA
7
8_554
hydrog
WATSON-CRICK
A
2ST
2
A
O4
2ST
2
1_555
A
DA
7
A
N6
DA
7
8_554
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
DC
6
A
N3
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
DC
6
A
O2
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
DC
6
A
N4
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
5
A
N3
DC
5
8_554
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
5
A
O2
DC
5
8_554
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
5
A
N4
DC
5
8_554
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
4
A
N1
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
4
A
O6
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
4
A
N2
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
3
A
N1
DG
3
8_554
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
3
A
O6
DG
3
8_554
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
3
A
N2
DG
3
8_554
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
A
2ST
2
A
N3
2ST
2
8_554
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
A
2ST
2
A
O4
2ST
2
8_554
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
A
DG
1
A
N1
DG
1
8_554
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
8_554
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
A
DG
1
A
N2
DG
1
8_554
DNA
selenium modification to facilitate crystallization, DNA
4H5A
PDB
1
4H5A
1
8
4H5A
1
8
4H5A
A
1
1
8
BINDING SITE FOR RESIDUE PT A 101
A
PT
101
Software
2
A
DG
4
A
DG
4
2
1_555
A
HOH
220
C
HOH
2
1_555
96
P 43 21 2