0.021030
0.000000
0.007123
0.000000
0.030469
0.000000
0.000000
0.000000
0.020049
0.00000
0.00000
0.00000
Kondo, J.
Francois, B.
Russell, R.J.M.
Murray, J.B.
Westhof, E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
108.710
90.000
47.550
32.820
52.660
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C22 H43 N5 O13
585.603
(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
AMIKACIN
non-polymer
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
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
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
R
C
N
39
R
C
N
40
S
C
N
41
S
C
N
42
R
C
N
43
N
C
N
44
N
O
N
45
N
O
N
46
N
O
N
47
N
N
N
48
R
C
N
49
N
N
N
50
N
C
N
51
S
C
N
52
N
N
N
53
R
C
N
54
S
C
N
55
N
O
N
56
S
C
N
57
N
O
N
58
S
C
N
59
R
C
N
60
N
O
N
61
S
C
N
62
N
N
N
63
S
C
N
64
N
O
N
65
R
C
N
66
N
O
N
67
N
C
N
68
N
O
N
69
N
O
N
70
N
O
N
71
N
N
N
72
N
C
N
73
N
O
N
74
S
C
N
75
N
C
N
76
N
C
N
77
N
O
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
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
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
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
O
N
122
N
P
N
123
N
O
N
124
N
O
N
125
N
O
N
126
N
C
N
127
R
C
N
128
N
O
N
129
S
C
N
130
N
O
N
131
R
C
N
132
N
O
N
133
R
C
N
134
N
N
N
135
N
C
N
136
N
O
N
137
N
N
N
138
N
C
N
139
N
N
N
140
N
C
N
141
N
C
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
H
N
154
N
H
N
155
N
H
N
156
N
O
N
157
N
P
N
158
N
O
N
159
N
O
N
160
N
O
N
161
N
C
N
162
R
C
N
163
N
O
N
164
S
C
N
165
N
O
N
166
R
C
N
167
N
O
N
168
R
C
Y
169
N
N
Y
170
N
C
Y
171
N
N
Y
172
N
C
N
173
N
C
N
174
N
O
N
175
N
N
N
176
N
C
N
177
N
N
N
178
N
N
Y
179
N
C
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
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
O
N
195
N
H
N
196
N
H
N
197
N
O
N
198
N
P
N
199
N
O
N
200
N
O
N
201
N
O
N
202
N
C
N
203
R
C
N
204
N
O
N
205
S
C
N
206
N
O
N
207
R
C
N
208
N
O
N
209
R
C
N
210
N
N
N
211
N
C
N
212
N
O
N
213
N
N
N
214
N
C
N
215
N
O
N
216
N
C
N
217
N
C
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
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
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
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
doub
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
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
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
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
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
doub
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
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
doub
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
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
Y
185
N
sing
Y
186
N
sing
Y
187
N
doub
N
188
N
sing
Y
189
N
sing
N
190
N
sing
Y
191
N
doub
N
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
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
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
doub
N
234
N
sing
N
235
N
doub
N
236
N
sing
N
237
N
sing
FR
Biochimie
BICMBE
0466
0300-9084
88
1027
1031
10.1016/j.biochi.2006.05.017
16806634
Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.
2006
10.2210/pdb4p20/pdb
pdb_00004p20
100
1
CCD
2004-06-26
ADSC QUANTUM 4
SINGLE WAVELENGTH
x-ray
1
0.9357
1.0
ID14-4
ESRF
0.9357
SYNCHROTRON
ESRF BEAMLINE ID14-4
7355.409
5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
2
syn
polymer
585.603
(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
2
syn
non-polymer
18.015
water
75
nat
water
no
no
UUGCGUCACACCGGUGAAGUCGC
UUGCGUCACACCGGUGAAGUCGC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.65
53.51
VAPOR DIFFUSION
6.4
MPF, Na Cacodylate, NaCl, KCl
310
3.829
1
19
A
2
B
44
1.850
A_G2:C44_B
1
-7.384
-0.192
0.383
-0.153
-1.454
1
19
A
3
B
43
-1.760
A_C3:G43_B
2
-12.569
0.090
0.267
-0.025
3.609
1
19
A
4
B
42
1.583
A_G4:C42_B
3
-5.903
-0.317
0.040
-0.010
10.070
A
5
B
41
-27.554
A_U5:U41_B
4
-9.261
-2.758
-1.270
-1.071
-5.086
1
19
A
6
B
40
-1.470
A_C6:G40_B
5
-0.342
0.373
-0.196
-0.208
7.101
1
19
A
8
B
37
0.320
A_C8:G37_B
6
-20.838
0.214
0.011
-0.132
1.076
1
20
A
9
B
36
1.939
A_A9:U36_B
7
-18.388
0.124
-0.161
-0.080
6.331
1
19
A
10
B
35
-0.089
A_C10:G35_B
8
-18.283
0.296
0.056
-0.190
-2.146
1
19
A
11
B
34
2.117
A_C11:G34_B
9
-4.110
0.053
0.442
-0.122
-0.590
1
19
A
12
B
33
-0.388
A_G12:C33_B
10
-9.055
-0.076
0.319
-0.109
-5.961
1
19
A
13
B
32
2.168
A_G13:C32_B
11
-17.569
-0.049
-0.107
-0.018
4.930
1
20
A
14
B
31
0.705
A_U14:A31_B
12
-11.392
-0.015
-0.137
-0.131
-15.766
1
19
A
15
B
30
0.003
A_G15:C30_B
13
-25.962
-0.335
-0.052
-0.046
4.399
1
19
A
18
B
28
-2.127
A_G18:C28_B
14
1.924
-0.242
-0.233
-0.229
1.451
A
19
B
27
-28.908
A_U19:U27_B
15
-6.581
2.017
-0.475
-1.312
4.101
1
19
A
20
B
26
-0.239
A_C20:G26_B
16
-0.051
0.325
-0.129
-0.251
-2.854
1
19
A
21
B
25
3.969
A_G21:C25_B
17
-2.231
-0.152
0.226
-0.052
-0.635
1
19
A
22
B
24
6.447
A_C22:G24_B
18
-3.250
0.365
0.434
-0.076
3.313
34.126
A
A
2
3
3.396
B
B
44
43
3.416
1.992
-0.342
-1.866
AA_G2C3:G43C44_BB
1
-0.982
1.675
34.056
-3.506
0.422
2.461
28.287
A
A
3
4
13.136
B
B
43
42
2.969
6.366
-0.301
-1.947
AA_C3G4:C42G43_BB
2
0.498
-1.027
27.571
-5.226
0.713
2.314
20.150
A
A
4
5
10.661
B
B
42
41
3.212
3.628
-0.712
-2.139
AA_G4U5:U41C42_BB
3
7.205
-21.176
18.480
-7.584
4.954
3.545
47.141
A
A
5
6
5.578
B
B
41
40
4.004
4.448
2.036
-2.448
AA_U5C6:G40U41_BB
4
-5.027
6.305
46.687
-3.483
-3.023
5.592
79.009
A
A
6
8
11.286
B
B
40
37
6.352
14.274
1.314
-3.303
AA_C6C8:G37G40_BB
5
-10.294
8.139
77.339
-3.317
-1.553
2.283
34.127
A
A
8
9
27.653
B
B
37
36
3.340
15.652
-0.071
-1.563
AA_C8A9:U36G37_BB
6
1.036
-1.831
30.404
-4.930
0.271
2.925
31.539
A
A
9
10
5.743
B
B
36
35
3.109
3.116
0.670
-1.825
AA_A9C10:G35U36_BB
7
0.305
-0.563
31.387
-3.894
-1.180
3.272
31.260
A
A
10
11
7.365
B
B
35
34
3.496
3.943
-0.628
-2.050
AA_C10C11:G34G35_BB
8
-4.864
9.086
30.642
-4.584
0.202
2.630
31.215
A
A
11
12
13.191
B
B
34
33
3.072
7.040
-0.125
-1.656
AA_C11G12:C33G34_BB
9
0.295
-0.552
30.429
-4.259
0.281
2.710
34.694
A
A
12
13
16.297
B
B
33
32
3.236
9.563
0.391
-1.598
AA_G12G13:C32C33_BB
10
5.249
-8.945
32.985
-4.049
0.096
3.194
29.168
A
A
13
14
-3.543
B
B
32
31
3.108
-1.783
-0.163
-1.509
AA_G13U14:A31C32_BB
11
-0.267
0.531
29.114
-2.622
0.267
2.259
40.363
A
A
14
15
33.729
B
B
31
30
3.559
22.078
0.390
-1.453
AA_U14G15:C30A31_BB
12
2.059
-3.146
33.941
-4.531
-0.338
5.336
77.633
A
A
15
18
11.823
B
B
30
28
6.085
14.748
-1.554
-3.469
AA_G15G18:C28C30_BB
13
5.801
-4.650
76.250
-3.506
1.530
3.620
45.371
A
A
18
19
-2.495
B
B
28
27
3.553
-1.924
-1.645
-2.417
AA_G18U19:U27C28_BB
14
0.779
-1.010
45.326
-2.947
2.209
2.177
24.053
A
A
19
20
20.536
B
B
27
26
3.293
8.383
0.674
-2.647
AA_U19C20:G26U27_BB
15
-0.172
0.421
22.565
-8.680
-1.665
2.869
28.502
A
A
20
21
11.269
B
B
26
25
3.288
5.512
0.737
-1.668
AA_C20G21:C25G26_BB
16
-1.505
3.078
27.935
-4.585
-1.823
3.194
34.640
A
A
21
22
-1.019
B
B
25
24
3.149
-0.607
0.374
-2.243
AA_G21C22:G24C25_BB
17
0.826
-1.387
34.625
-3.676
-0.505
citation
pdbx_database_status
pdbx_entity_src_syn
pdbx_struct_assembly
pdbx_struct_oper_list
software
struct_keywords
chem_comp
chem_comp_atom
chem_comp_bond
database_2
entity
pdbx_entity_nonpoly
refine_hist
repository
Initial release
Database references
Database references
Derived calculations
Other
Refinement description
Source and taxonomy
Structure summary
Data collection
Database references
Derived calculations
Refinement description
Structure summary
1
0
2014-05-07
1
1
2015-01-07
1
2
2017-11-22
1
3
2023-12-27
_citation.journal_id_CSD
_pdbx_database_status.pdb_format_compatible
_pdbx_entity_src_syn.pdbx_alt_source_flag
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_oper_list.symmetry_operation
_struct_keywords.text
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_refine_hist.number_atoms_total
_refine_hist.pdbx_number_atoms_nucleic_acid
_refine_hist.pdbx_number_atoms_protein
2014-05-07
SPRSDE
N
RCSB
Y
RCSB
2014-02-28
REL
REL
1
B
O
HOH
223
5.86
AKN
(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
HOH
water
32630
synthetic construct
sample
1
23
AMI
52
2
AKN
AKN
101
A
AMI
51
2
AKN
AKN
101
B
HOH
153
3
HOH
HOH
201
A
HOH
118
3
HOH
HOH
202
A
HOH
149
3
HOH
HOH
203
A
HOH
131
3
HOH
HOH
204
A
HOH
162
3
HOH
HOH
205
A
HOH
154
3
HOH
HOH
206
A
HOH
175
3
HOH
HOH
207
A
HOH
155
3
HOH
HOH
208
A
HOH
174
3
HOH
HOH
209
A
HOH
166
3
HOH
HOH
210
A
HOH
168
3
HOH
HOH
211
A
HOH
102
3
HOH
HOH
212
A
HOH
108
3
HOH
HOH
213
A
HOH
110
3
HOH
HOH
214
A
HOH
112
3
HOH
HOH
215
A
HOH
113
3
HOH
HOH
216
A
HOH
114
3
HOH
HOH
217
A
HOH
115
3
HOH
HOH
218
A
HOH
121
3
HOH
HOH
219
A
HOH
122
3
HOH
HOH
220
A
HOH
123
3
HOH
HOH
221
A
HOH
124
3
HOH
HOH
222
A
HOH
125
3
HOH
HOH
223
A
HOH
128
3
HOH
HOH
224
A
HOH
129
3
HOH
HOH
225
A
HOH
130
3
HOH
HOH
226
A
HOH
135
3
HOH
HOH
227
A
HOH
136
3
HOH
HOH
228
A
HOH
139
3
HOH
HOH
229
A
HOH
143
3
HOH
HOH
230
A
HOH
158
3
HOH
HOH
231
A
HOH
160
3
HOH
HOH
232
A
HOH
171
3
HOH
HOH
233
A
HOH
172
3
HOH
HOH
234
A
HOH
176
3
HOH
HOH
235
A
HOH
104
3
HOH
HOH
201
B
HOH
159
3
HOH
HOH
202
B
HOH
148
3
HOH
HOH
203
B
HOH
134
3
HOH
HOH
204
B
HOH
120
3
HOH
HOH
205
B
HOH
150
3
HOH
HOH
206
B
HOH
117
3
HOH
HOH
207
B
HOH
127
3
HOH
HOH
208
B
HOH
107
3
HOH
HOH
209
B
HOH
142
3
HOH
HOH
210
B
HOH
152
3
HOH
HOH
211
B
HOH
119
3
HOH
HOH
212
B
HOH
133
3
HOH
HOH
213
B
HOH
170
3
HOH
HOH
214
B
HOH
161
3
HOH
HOH
215
B
HOH
145
3
HOH
HOH
216
B
HOH
169
3
HOH
HOH
217
B
HOH
101
3
HOH
HOH
218
B
HOH
103
3
HOH
HOH
219
B
HOH
105
3
HOH
HOH
220
B
HOH
106
3
HOH
HOH
221
B
HOH
109
3
HOH
HOH
222
B
HOH
116
3
HOH
HOH
223
B
HOH
126
3
HOH
HOH
224
B
HOH
132
3
HOH
HOH
225
B
HOH
137
3
HOH
HOH
226
B
HOH
138
3
HOH
HOH
227
B
HOH
140
3
HOH
HOH
228
B
HOH
141
3
HOH
HOH
229
B
HOH
144
3
HOH
HOH
230
B
HOH
146
3
HOH
HOH
231
B
HOH
147
3
HOH
HOH
232
B
HOH
151
3
HOH
HOH
233
B
HOH
156
3
HOH
HOH
234
B
HOH
157
3
HOH
HOH
235
B
HOH
163
3
HOH
HOH
236
B
HOH
164
3
HOH
HOH
237
B
HOH
165
3
HOH
HOH
238
B
HOH
167
3
HOH
HOH
239
B
HOH
173
3
HOH
HOH
240
B
n
1
0
A
n
2
1
A
G
2
n
3
G
2
A
C
3
n
4
C
3
A
G
4
n
5
G
4
A
U
5
n
6
U
5
A
C
6
n
7
C
6
A
A
7
n
8
A
7
A
C
8
n
9
C
8
A
A
9
n
10
A
9
A
C
10
n
11
C
10
A
C
11
n
12
C
11
A
G
12
n
13
G
12
A
G
13
n
14
G
13
A
U
14
n
15
U
14
A
G
15
n
16
G
15
A
A
16
n
17
A
16
A
A
17
n
18
A
17
A
G
18
n
19
G
18
A
U
19
n
20
U
19
A
C
20
n
21
C
20
A
G
21
n
22
G
21
A
C
22
n
23
C
22
A
n
1
22
B
n
2
23
B
G
24
n
3
G
24
B
C
25
n
4
C
25
B
G
26
n
5
G
26
B
U
27
n
6
U
27
B
C
28
n
7
C
28
B
A
29
n
8
A
29
B
C
30
n
9
C
30
B
A
31
n
10
A
31
B
C
32
n
11
C
32
B
C
33
n
12
C
33
B
G
34
n
13
G
34
B
G
35
n
14
G
35
B
U
36
n
15
U
36
B
G
37
n
16
G
37
B
A
38
n
17
A
38
B
A
39
n
18
A
39
B
G
40
n
19
G
40
B
U
41
n
20
U
41
B
C
42
n
21
C
42
B
G
43
n
22
G
43
B
C
44
n
23
C
44
B
software_defined_assembly
PISA
2
dimeric
4210
-23
7660
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
U
0
A
U
1
1
Y
1
A
U
1
A
U
2
1
Y
1
B
U
22
B
U
1
1
Y
1
B
U
23
B
U
2
1
Y
1
A
U
5
0.071
SIDE CHAIN
CNS_TOPPAR:protein_rep.param
CNS_TOPPAR:dna-rna_rep.param
CNS_TOPPAR:water_rep.param
CNS_TOPPAR:ion.param
amika_xplor.param
120.730
45.5528
10.200
-9.8000
0.0000
11.5700
1.7740
0.0000
8.0260
0.2679
0.2134
2.7000
10.0000
425
3693
4118
9.9000
95.7000
0.8070
1
FREE R-VALUE
179.000
MOLECULAR REPLACEMENT
64.5977
2.7000
10.0000
75
1053
42.97
39.55
80
898
0
42
0.000
1.500
5.008
2.000
0.000
2.000
6.969
2.500
2.700
32.820
4P20
4398
0.160
0.960
1
4.800
15897
3.590
120
100.000
0.432
2.700
2.800
2.000
1607
445
0.590
1
3.610
0
100.000
0.304
2.800
2.910
2.600
1555
424
0.610
1
3.670
0
100.000
0.269
2.910
3.040
2.800
1578
431
0.650
1
3.660
0
100.000
0.167
3.040
3.200
4.400
1596
434
0.920
1
3.660
7
100.000
0.151
3.200
3.400
5.200
1608
436
0.990
1
3.660
13
99.800
0.148
3.400
3.660
5.400
1646
447
1.010
1
3.630
22
99.800
0.130
3.660
4.030
7.200
1558
426
1.170
1
3.610
20
99.800
0.180
4.030
4.610
5.200
1599
439
1.240
1
3.620
8
100.000
0.159
4.610
5.810
5.900
1595
450
1.170
1
3.520
11
100.000
0.132
5.810
32.820
7.900
1555
466
1.320
1
3.250
39
100.000
phasing
AMoRE
refinement
CNS
data extraction
PDB_EXTRACT
Crystal structures of the bacterial ribosomal decoding site complexed with amikacin
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
A
G
2
A
N1
G
3
1_555
B
C
44
B
N3
C
23
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
3
1_555
B
C
44
B
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
3
1_555
B
C
44
B
N4
C
23
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
4
1_555
B
G
43
B
N1
G
22
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
4
1_555
B
G
43
B
O6
G
22
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
4
1_555
B
G
43
B
N2
G
22
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
5
1_555
B
C
42
B
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
5
1_555
B
C
42
B
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
5
1_555
B
C
42
B
N4
C
21
1_555
hydrog
U-U MISPAIR
A
U
5
A
O4
U
6
1_555
B
U
41
B
N3
U
20
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
7
1_555
B
G
40
B
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
7
1_555
B
G
40
B
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
7
1_555
B
G
40
B
N2
G
19
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
9
1_555
B
G
37
B
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
9
1_555
B
G
37
B
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
9
1_555
B
G
37
B
N2
G
16
1_555
hydrog
WATSON-CRICK
A
A
9
A
N1
A
10
1_555
B
U
36
B
N3
U
15
1_555
hydrog
WATSON-CRICK
A
A
9
A
N6
A
10
1_555
B
U
36
B
O4
U
15
1_555
hydrog
WATSON-CRICK
A
C
10
A
N3
C
11
1_555
B
G
35
B
N1
G
14
1_555
hydrog
WATSON-CRICK
A
C
10
A
N4
C
11
1_555
B
G
35
B
O6
G
14
1_555
hydrog
WATSON-CRICK
A
C
10
A
O2
C
11
1_555
B
G
35
B
N2
G
14
1_555
hydrog
WATSON-CRICK
A
C
11
A
N3
C
12
1_555
B
G
34
B
N1
G
13
1_555
hydrog
WATSON-CRICK
A
C
11
A
N4
C
12
1_555
B
G
34
B
O6
G
13
1_555
hydrog
WATSON-CRICK
A
C
11
A
O2
C
12
1_555
B
G
34
B
N2
G
13
1_555
hydrog
WATSON-CRICK
A
G
12
A
N1
G
13
1_555
B
C
33
B
N3
C
12
1_555
hydrog
WATSON-CRICK
A
G
12
A
N2
G
13
1_555
B
C
33
B
O2
C
12
1_555
hydrog
WATSON-CRICK
A
G
12
A
O6
G
13
1_555
B
C
33
B
N4
C
12
1_555
hydrog
WATSON-CRICK
A
G
13
A
N1
G
14
1_555
B
C
32
B
N3
C
11
1_555
hydrog
WATSON-CRICK
A
G
13
A
N2
G
14
1_555
B
C
32
B
O2
C
11
1_555
hydrog
WATSON-CRICK
A
G
13
A
O6
G
14
1_555
B
C
32
B
N4
C
11
1_555
hydrog
WATSON-CRICK
A
U
14
A
N3
U
15
1_555
B
A
31
B
N1
A
10
1_555
hydrog
WATSON-CRICK
A
U
14
A
O4
U
15
1_555
B
A
31
B
N6
A
10
1_555
hydrog
WATSON-CRICK
A
G
15
A
N1
G
16
1_555
B
C
30
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
15
A
N2
G
16
1_555
B
C
30
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
15
A
O6
G
16
1_555
B
C
30
B
N4
C
9
1_555
hydrog
WATSON-CRICK
A
G
18
A
N1
G
19
1_555
B
C
28
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
18
A
N2
G
19
1_555
B
C
28
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
18
A
O6
G
19
1_555
B
C
28
B
N4
C
7
1_555
hydrog
U-U MISPAIR
A
U
19
A
N3
U
20
1_555
B
U
27
B
O4
U
6
1_555
hydrog
WATSON-CRICK
A
C
20
A
N3
C
21
1_555
B
G
26
B
N1
G
5
1_555
hydrog
WATSON-CRICK
A
C
20
A
N4
C
21
1_555
B
G
26
B
O6
G
5
1_555
hydrog
WATSON-CRICK
A
C
20
A
O2
C
21
1_555
B
G
26
B
N2
G
5
1_555
hydrog
WATSON-CRICK
A
G
21
A
N1
G
22
1_555
B
C
25
B
N3
C
4
1_555
hydrog
WATSON-CRICK
A
G
21
A
N2
G
22
1_555
B
C
25
B
O2
C
4
1_555
hydrog
WATSON-CRICK
A
G
21
A
O6
G
22
1_555
B
C
25
B
N4
C
4
1_555
hydrog
WATSON-CRICK
A
C
22
A
N3
C
23
1_555
B
G
24
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
22
A
N4
C
23
1_555
B
G
24
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
22
A
O2
C
23
1_555
B
G
24
B
N2
G
3
1_555
RNA/ANTIBIOTIC
AMINOGLYCOSIDE, HABA GROUP, RIBOSOMAL DECODING SITE, X-RAY ANALYSIS, RNA, AMIKACIN, RNA-ANTIBIOTIC complex
4P20
PDB
1
4P20
0
22
4P20
0
22
4P20
A
1
1
23
22
44
4P20
22
44
4P20
B
1
1
23
binding site for residue AKN A 101
A
AKN
101
Software
15
binding site for residue AKN B 101
B
AKN
101
Software
16
A
G
15
A
G
16
15
1_555
A
A
16
A
A
17
15
1_555
A
A
17
A
A
18
15
1_555
A
G
18
A
G
19
15
1_555
A
U
19
A
U
20
15
1_555
A
C
20
A
C
21
15
1_555
A
G
21
A
G
22
15
1_555
A
C
22
A
C
23
15
1_555
A
HOH
233
E
HOH
15
1_555
B
G
24
B
G
3
15
1_555
B
C
25
B
C
4
15
1_555
B
G
26
B
G
5
15
1_555
B
U
27
B
U
6
15
1_555
B
C
28
B
C
7
15
1_555
B
A
29
B
A
8
15
1_555
A
G
2
A
G
3
16
1_555
A
C
3
A
C
4
16
1_555
A
G
4
A
G
5
16
1_555
A
C
6
A
C
7
16
1_555
A
A
7
A
A
8
16
1_555
B
G
37
B
G
16
16
1_555
B
A
38
B
A
17
16
1_555
B
A
39
B
A
18
16
1_555
B
G
40
B
G
19
16
1_555
B
U
41
B
U
20
16
1_555
B
C
42
B
C
21
16
1_555
B
G
43
B
G
22
16
1_555
B
C
44
B
C
23
16
1_555
B
HOH
203
F
HOH
16
1_555
B
HOH
207
F
HOH
16
1_555
B
HOH
222
F
HOH
16
1_555
4
P 1 21 1