0.020325
0.011735
0.000000
0.000000
0.023470
0.000000
0.000000
0.000000
0.010081
0.00000
0.00000
0.00000
Dyer, D.H.
Rubio, L.M.
Thoden, J.B.
Holden, H.M.
Ludden, P.W.
Rayment, I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
49.200
49.200
99.200
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
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
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
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
C
N
89
N
O
N
90
N
C
N
91
N
O
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
N
N
99
S
C
N
100
N
C
N
101
N
O
N
102
N
C
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
N
N
107
N
O
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
N
N
119
S
C
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
C
N
124
N
C
N
125
N
O
N
126
N
O
N
127
N
O
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
N
N
138
N
C
N
139
N
C
N
140
N
O
N
141
N
O
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
N
C
Y
152
N
C
Y
153
N
N
Y
154
N
C
Y
155
N
C
Y
156
N
N
N
157
N
O
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
O
N
169
N
H
N
170
N
H
N
171
N
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
S
C
N
176
N
C
N
177
N
C
N
178
N
C
N
179
N
O
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
N
N
194
S
C
N
195
N
C
N
196
N
O
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
C
N
201
N
O
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
C
N
223
N
N
N
224
N
O
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
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
N
N
241
S
C
N
242
N
C
N
243
N
O
N
244
N
C
N
245
N
C
N
246
N
S
N
247
N
C
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
Y
270
N
C
N
271
N
O
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
C
N
289
N
C
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
N
N
301
S
C
N
302
N
C
N
303
N
O
N
304
N
C
N
305
N
O
N
306
N
O
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
R
C
N
319
N
O
N
320
N
C
N
321
N
O
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
N
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
N
345
N
O
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
N
369
N
O
N
370
N
O
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
O
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
doub
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
doub
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
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
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
sing
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
N
97
N
sing
N
98
N
doub
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
doub
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
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
doub
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
doub
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
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
Y
149
N
sing
Y
150
N
doub
Y
151
N
doub
N
152
N
sing
Y
153
N
sing
N
154
N
sing
Y
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
doub
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
sing
N
187
N
sing
N
188
N
doub
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
doub
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
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
doub
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
Y
257
N
doub
Y
258
N
sing
Y
259
N
sing
N
260
N
sing
Y
261
N
doub
N
262
N
sing
Y
263
N
doub
N
264
N
sing
Y
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
doub
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
doub
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
Y
326
N
doub
Y
327
N
sing
Y
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
doub
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
Y
354
N
doub
Y
355
N
sing
Y
356
N
sing
N
357
N
sing
Y
358
N
doub
N
359
N
sing
Y
360
N
doub
N
361
N
sing
Y
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
278
32150
32156
10.1074/jbc.M304264200
12754195
The Three-dimensional Structure of the Core Domain of NafY from Azotobacter vinelandii determined at 1.8 A resolution
2003
10.2210/pdb1p90/pdb
pdb_00001p90
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
120
1
CCD
2002-03-01
CUSTOM-MADE
SINGLE WAVELENGTH
M
x-ray
1
0.97
1.0
19-ID
APS
0.97
SYNCHROTRON
APS BEAMLINE 19-ID
15514.565
hypothetical protein
core domain
1
man
polymer
62.068
1,2-ETHANEDIOL
1
syn
non-polymer
18.015
water
174
nat
water
NafY protein
no
no
ERVPEGSIRVAIASNNGEQLDGHFGSCLRFLVYQVSAKDASLVDIRSTLDVALAEDKNAWRVEQIQDCQVLYVVSIGGPA
AAKVVRAGIHPLKKPKGCAAQEAIAELQTVMAGSPPPWLAKLVGVSAEERVRFSVSDDEDEAARA
ERVPEGSIRVAIASNNGEQLDGHFGSCLRFLVYQVSAKDASLVDIRSTLDVALAEDKNAWRVEQIQDCQVLYVVSIGGPA
AAKVVRAGIHPLKKPKGCAAQEAIAELQTVMAGSPPPWLAKLVGVSAEERVRFSVSDDEDEAARA
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Azotobacter
Escherichia
sample
NafY
354
Azotobacter vinelandii
562
Escherichia coli
1
2.23
44.92
VAPOR DIFFUSION, HANGING DROP
8.5
3 ml of NafY protein at 10 mg/ml combined with an equal volume of 13% PEG 10000, 2.5% glycerol, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-08-19
1
1
2008-04-29
1
2
2011-07-13
1
3
2024-02-14
_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
2003-05-08
REL
REL
EDO
1,2-ETHANEDIOL
HOH
water
EG
300
2
EDO
EDO
300
A
HOH
400
3
HOH
HOH
400
A
HOH
402
3
HOH
HOH
402
A
HOH
403
3
HOH
HOH
403
A
HOH
404
3
HOH
HOH
404
A
HOH
405
3
HOH
HOH
405
A
HOH
406
3
HOH
HOH
406
A
HOH
407
3
HOH
HOH
407
A
HOH
409
3
HOH
HOH
409
A
HOH
410
3
HOH
HOH
410
A
HOH
411
3
HOH
HOH
411
A
HOH
413
3
HOH
HOH
413
A
HOH
414
3
HOH
HOH
414
A
HOH
416
3
HOH
HOH
416
A
HOH
417
3
HOH
HOH
417
A
HOH
418
3
HOH
HOH
418
A
HOH
419
3
HOH
HOH
419
A
HOH
421
3
HOH
HOH
421
A
HOH
422
3
HOH
HOH
422
A
HOH
423
3
HOH
HOH
423
A
HOH
425
3
HOH
HOH
425
A
HOH
427
3
HOH
HOH
427
A
HOH
428
3
HOH
HOH
428
A
HOH
429
3
HOH
HOH
429
A
HOH
430
3
HOH
HOH
430
A
HOH
431
3
HOH
HOH
431
A
HOH
432
3
HOH
HOH
432
A
HOH
433
3
HOH
HOH
433
A
HOH
434
3
HOH
HOH
434
A
HOH
436
3
HOH
HOH
436
A
HOH
437
3
HOH
HOH
437
A
HOH
438
3
HOH
HOH
438
A
HOH
439
3
HOH
HOH
439
A
HOH
441
3
HOH
HOH
441
A
HOH
443
3
HOH
HOH
443
A
HOH
445
3
HOH
HOH
445
A
HOH
446
3
HOH
HOH
446
A
HOH
452
3
HOH
HOH
452
A
HOH
454
3
HOH
HOH
454
A
HOH
455
3
HOH
HOH
455
A
HOH
456
3
HOH
HOH
456
A
HOH
460
3
HOH
HOH
460
A
HOH
465
3
HOH
HOH
465
A
HOH
467
3
HOH
HOH
467
A
HOH
468
3
HOH
HOH
468
A
HOH
471
3
HOH
HOH
471
A
HOH
472
3
HOH
HOH
472
A
HOH
474
3
HOH
HOH
474
A
HOH
475
3
HOH
HOH
475
A
HOH
477
3
HOH
HOH
477
A
HOH
478
3
HOH
HOH
478
A
HOH
600
3
HOH
HOH
600
A
HOH
601
3
HOH
HOH
601
A
HOH
602
3
HOH
HOH
602
A
HOH
603
3
HOH
HOH
603
A
HOH
604
3
HOH
HOH
604
A
HOH
605
3
HOH
HOH
605
A
HOH
606
3
HOH
HOH
606
A
HOH
607
3
HOH
HOH
607
A
HOH
608
3
HOH
HOH
608
A
HOH
609
3
HOH
HOH
609
A
HOH
610
3
HOH
HOH
610
A
HOH
611
3
HOH
HOH
611
A
HOH
612
3
HOH
HOH
612
A
HOH
614
3
HOH
HOH
614
A
HOH
615
3
HOH
HOH
615
A
HOH
616
3
HOH
HOH
616
A
HOH
617
3
HOH
HOH
617
A
HOH
619
3
HOH
HOH
619
A
HOH
620
3
HOH
HOH
620
A
HOH
622
3
HOH
HOH
622
A
HOH
623
3
HOH
HOH
623
A
HOH
624
3
HOH
HOH
624
A
HOH
625
3
HOH
HOH
625
A
HOH
626
3
HOH
HOH
626
A
HOH
627
3
HOH
HOH
627
A
HOH
628
3
HOH
HOH
628
A
HOH
632
3
HOH
HOH
632
A
HOH
633
3
HOH
HOH
633
A
HOH
635
3
HOH
HOH
635
A
HOH
636
3
HOH
HOH
636
A
HOH
637
3
HOH
HOH
637
A
HOH
638
3
HOH
HOH
638
A
HOH
639
3
HOH
HOH
639
A
HOH
642
3
HOH
HOH
642
A
HOH
645
3
HOH
HOH
645
A
HOH
646
3
HOH
HOH
646
A
HOH
647
3
HOH
HOH
647
A
HOH
648
3
HOH
HOH
648
A
HOH
650
3
HOH
HOH
650
A
HOH
652
3
HOH
HOH
652
A
HOH
654
3
HOH
HOH
654
A
HOH
655
3
HOH
HOH
655
A
HOH
656
3
HOH
HOH
656
A
HOH
660
3
HOH
HOH
660
A
HOH
662
3
HOH
HOH
662
A
HOH
663
3
HOH
HOH
663
A
HOH
664
3
HOH
HOH
664
A
HOH
665
3
HOH
HOH
665
A
HOH
666
3
HOH
HOH
666
A
HOH
667
3
HOH
HOH
667
A
HOH
669
3
HOH
HOH
669
A
HOH
670
3
HOH
HOH
670
A
HOH
674
3
HOH
HOH
674
A
HOH
675
3
HOH
HOH
675
A
HOH
678
3
HOH
HOH
678
A
HOH
679
3
HOH
HOH
679
A
HOH
680
3
HOH
HOH
680
A
HOH
681
3
HOH
HOH
681
A
HOH
685
3
HOH
HOH
685
A
HOH
695
3
HOH
HOH
695
A
HOH
697
3
HOH
HOH
697
A
HOH
698
3
HOH
HOH
698
A
HOH
707
3
HOH
HOH
707
A
HOH
711
3
HOH
HOH
711
A
HOH
900
3
HOH
HOH
900
A
HOH
901
3
HOH
HOH
901
A
HOH
902
3
HOH
HOH
902
A
HOH
903
3
HOH
HOH
903
A
HOH
905
3
HOH
HOH
905
A
HOH
907
3
HOH
HOH
907
A
HOH
909
3
HOH
HOH
909
A
HOH
910
3
HOH
HOH
910
A
HOH
911
3
HOH
HOH
911
A
HOH
913
3
HOH
HOH
913
A
HOH
914
3
HOH
HOH
914
A
HOH
915
3
HOH
HOH
915
A
HOH
916
3
HOH
HOH
916
A
HOH
917
3
HOH
HOH
917
A
HOH
919
3
HOH
HOH
919
A
HOH
920
3
HOH
HOH
920
A
HOH
923
3
HOH
HOH
923
A
HOH
925
3
HOH
HOH
925
A
HOH
928
3
HOH
HOH
928
A
HOH
932
3
HOH
HOH
932
A
HOH
933
3
HOH
HOH
933
A
HOH
934
3
HOH
HOH
934
A
HOH
936
3
HOH
HOH
936
A
HOH
937
3
HOH
HOH
937
A
HOH
940
3
HOH
HOH
940
A
HOH
941
3
HOH
HOH
941
A
HOH
942
3
HOH
HOH
942
A
HOH
943
3
HOH
HOH
943
A
HOH
944
3
HOH
HOH
944
A
HOH
945
3
HOH
HOH
945
A
HOH
950
3
HOH
HOH
950
A
HOH
1100
3
HOH
HOH
1100
A
HOH
1101
3
HOH
HOH
1101
A
HOH
1102
3
HOH
HOH
1102
A
HOH
1103
3
HOH
HOH
1103
A
HOH
1104
3
HOH
HOH
1104
A
HOH
1105
3
HOH
HOH
1105
A
HOH
1106
3
HOH
HOH
1106
A
HOH
1107
3
HOH
HOH
1107
A
HOH
1108
3
HOH
HOH
1108
A
HOH
1109
3
HOH
HOH
1109
A
HOH
1110
3
HOH
HOH
1110
A
HOH
1111
3
HOH
HOH
1111
A
HOH
1114
3
HOH
HOH
1114
A
HOH
1304
3
HOH
HOH
1304
A
HOH
1305
3
HOH
HOH
1305
A
HOH
1306
3
HOH
HOH
1306
A
HOH
1307
3
HOH
HOH
1307
A
HOH
1308
3
HOH
HOH
1308
A
HOH
1309
3
HOH
HOH
1309
A
HOH
1310
3
HOH
HOH
1310
A
HOH
1311
3
HOH
HOH
1311
A
HOH
1312
3
HOH
HOH
1312
A
HOH
1313
3
HOH
HOH
1313
A
HOH
1314
3
HOH
HOH
1314
A
HOH
1316
3
HOH
HOH
1316
A
HOH
1317
3
HOH
HOH
1317
A
HOH
1318
3
HOH
HOH
1318
A
HOH
1319
3
HOH
HOH
1319
A
HOH
1320
3
HOH
HOH
1320
A
ALA
99
n
1
GLU
99
A
ARG
100
n
2
ARG
100
A
VAL
101
n
3
VAL
101
A
PRO
102
n
4
PRO
102
A
GLU
103
n
5
GLU
103
A
GLY
104
n
6
GLY
104
A
SER
105
n
7
SER
105
A
ILE
106
n
8
ILE
106
A
ARG
107
n
9
ARG
107
A
VAL
108
n
10
VAL
108
A
ALA
109
n
11
ALA
109
A
ILE
110
n
12
ILE
110
A
ALA
111
n
13
ALA
111
A
SER
112
n
14
SER
112
A
ASN
113
n
15
ASN
113
A
ASN
114
n
16
ASN
114
A
GLY
115
n
17
GLY
115
A
GLU
116
n
18
GLU
116
A
GLN
117
n
19
GLN
117
A
LEU
118
n
20
LEU
118
A
ASP
119
n
21
ASP
119
A
GLY
120
n
22
GLY
120
A
HIS
121
n
23
HIS
121
A
PHE
122
n
24
PHE
122
A
GLY
123
n
25
GLY
123
A
SER
124
n
26
SER
124
A
CYS
125
n
27
CYS
125
A
LEU
126
n
28
LEU
126
A
ARG
127
n
29
ARG
127
A
PHE
128
n
30
PHE
128
A
LEU
129
n
31
LEU
129
A
VAL
130
n
32
VAL
130
A
TYR
131
n
33
TYR
131
A
GLN
132
n
34
GLN
132
A
VAL
133
n
35
VAL
133
A
SER
134
n
36
SER
134
A
ALA
135
n
37
ALA
135
A
LYS
136
n
38
LYS
136
A
ASP
137
n
39
ASP
137
A
ALA
138
n
40
ALA
138
A
SER
139
n
41
SER
139
A
LEU
140
n
42
LEU
140
A
VAL
141
n
43
VAL
141
A
ASP
142
n
44
ASP
142
A
ILE
143
n
45
ILE
143
A
ARG
144
n
46
ARG
144
A
SER
145
n
47
SER
145
A
THR
146
n
48
THR
146
A
LEU
147
n
49
LEU
147
A
ASP
148
n
50
ASP
148
A
VAL
149
n
51
VAL
149
A
ALA
150
n
52
ALA
150
A
LEU
151
n
53
LEU
151
A
ALA
152
n
54
ALA
152
A
GLU
153
n
55
GLU
153
A
ASP
154
n
56
ASP
154
A
LYS
155
n
57
LYS
155
A
ASN
156
n
58
ASN
156
A
ALA
157
n
59
ALA
157
A
TRP
158
n
60
TRP
158
A
ARG
159
n
61
ARG
159
A
VAL
160
n
62
VAL
160
A
GLU
161
n
63
GLU
161
A
GLN
162
n
64
GLN
162
A
ILE
163
n
65
ILE
163
A
GLN
164
n
66
GLN
164
A
ASP
165
n
67
ASP
165
A
CYS
166
n
68
CYS
166
A
GLN
167
n
69
GLN
167
A
VAL
168
n
70
VAL
168
A
LEU
169
n
71
LEU
169
A
TYR
170
n
72
TYR
170
A
VAL
171
n
73
VAL
171
A
VAL
172
n
74
VAL
172
A
SER
173
n
75
SER
173
A
ILE
174
n
76
ILE
174
A
GLY
175
n
77
GLY
175
A
GLY
176
n
78
GLY
176
A
PRO
177
n
79
PRO
177
A
ALA
178
n
80
ALA
178
A
ALA
179
n
81
ALA
179
A
ALA
180
n
82
ALA
180
A
LYS
181
n
83
LYS
181
A
VAL
182
n
84
VAL
182
A
VAL
183
n
85
VAL
183
A
ARG
184
n
86
ARG
184
A
ALA
185
n
87
ALA
185
A
GLY
186
n
88
GLY
186
A
ILE
187
n
89
ILE
187
A
HIS
188
n
90
HIS
188
A
PRO
189
n
91
PRO
189
A
LEU
190
n
92
LEU
190
A
LYS
191
n
93
LYS
191
A
LYS
192
n
94
LYS
192
A
PRO
193
n
95
PRO
193
A
LYS
194
n
96
LYS
194
A
GLY
195
n
97
GLY
195
A
CYS
196
n
98
CYS
196
A
ALA
197
n
99
ALA
197
A
ALA
198
n
100
ALA
198
A
GLN
199
n
101
GLN
199
A
GLU
200
n
102
GLU
200
A
ALA
201
n
103
ALA
201
A
ILE
202
n
104
ILE
202
A
ALA
203
n
105
ALA
203
A
GLU
204
n
106
GLU
204
A
LEU
205
n
107
LEU
205
A
GLN
206
n
108
GLN
206
A
THR
207
n
109
THR
207
A
VAL
208
n
110
VAL
208
A
MET
209
n
111
MET
209
A
ALA
210
n
112
ALA
210
A
GLY
211
n
113
GLY
211
A
SER
212
n
114
SER
212
A
PRO
213
n
115
PRO
213
A
PRO
214
n
116
PRO
214
A
PRO
215
n
117
PRO
215
A
TRP
216
n
118
TRP
216
A
LEU
217
n
119
LEU
217
A
ALA
218
n
120
ALA
218
A
LYS
219
n
121
LYS
219
A
LEU
220
n
122
LEU
220
A
VAL
221
n
123
VAL
221
A
n
124
222
A
n
125
223
A
n
126
224
A
n
127
225
A
n
128
226
A
n
129
227
A
n
130
228
A
n
131
229
A
n
132
230
A
n
133
231
A
n
134
232
A
n
135
233
A
n
136
234
A
n
137
235
A
n
138
236
A
n
139
237
A
n
140
238
A
n
141
239
A
n
142
240
A
n
143
241
A
n
144
242
A
n
145
243
A
author_defined_assembly
1
monomeric
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
A
O
ASP
142
A
O
ASP
44
A
N
VAL
130
A
N
VAL
32
A
O
TYR
131
A
O
TYR
33
A
N
VAL
108
A
N
VAL
10
A
N
ALA
109
A
N
ALA
11
A
O
TYR
170
A
O
TYR
72
A
N
LEU
169
A
N
LEU
71
A
O
LEU
190
A
O
LEU
92
A
N
LEU
118
A
N
LEU
20
A
O
CYS
196
A
O
CYS
98
1
A
HOH
624
C
HOH
1
A
CG
GLU
99
A
CG
GLU
1
1
Y
1
A
CD
GLU
99
A
CD
GLU
1
1
Y
1
A
OE1
GLU
99
A
OE1
GLU
1
1
Y
1
A
OE2
GLU
99
A
OE2
GLU
1
1
Y
1
A
GLY
222
A
GLY
124
1
Y
1
A
VAL
223
A
VAL
125
1
Y
1
A
SER
224
A
SER
126
1
Y
1
A
ALA
225
A
ALA
127
1
Y
1
A
GLU
226
A
GLU
128
1
Y
1
A
GLU
227
A
GLU
129
1
Y
1
A
ARG
228
A
ARG
130
1
Y
1
A
VAL
229
A
VAL
131
1
Y
1
A
ARG
230
A
ARG
132
1
Y
1
A
PHE
231
A
PHE
133
1
Y
1
A
SER
232
A
SER
134
1
Y
1
A
VAL
233
A
VAL
135
1
Y
1
A
SER
234
A
SER
136
1
Y
1
A
ASP
235
A
ASP
137
1
Y
1
A
ASP
236
A
ASP
138
1
Y
1
A
GLU
237
A
GLU
139
1
Y
1
A
ASP
238
A
ASP
140
1
Y
1
A
GLU
239
A
GLU
141
1
Y
1
A
ALA
240
A
ALA
142
1
Y
1
A
ALA
241
A
ALA
143
1
Y
1
A
ARG
242
A
ARG
144
1
Y
1
A
ALA
243
A
ALA
145
1
Y
1
12.87
1.80
110.60
123.47
A
A
A
N
CA
CB
ARG
ARG
ARG
100
100
100
N
1
-6.19
0.90
118.30
112.11
A
A
A
CB
CG
OD2
ASP
ASP
ASP
119
119
119
N
1
5.56
0.50
120.30
125.86
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
127
127
127
N
1
-4.23
0.50
120.30
116.07
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
127
127
127
N
1
-5.60
0.90
118.30
112.70
A
A
A
CB
CG
OD2
ASP
ASP
ASP
137
137
137
A
A
A
N
1
-5.64
0.90
118.30
112.66
A
A
A
CB
CG
OD2
ASP
ASP
ASP
137
137
137
B
B
B
N
1
5.61
0.90
118.30
123.91
A
A
A
CB
CG
OD1
ASP
ASP
ASP
142
142
142
N
1
-5.60
0.90
118.30
112.70
A
A
A
CB
CG
OD2
ASP
ASP
ASP
148
148
148
N
1
5.99
0.90
118.30
124.29
A
A
A
CB
CG
OD1
ASP
ASP
ASP
154
154
154
A
A
A
N
1
-6.03
0.90
118.30
112.27
A
A
A
CB
CG
OD2
ASP
ASP
ASP
154
154
154
B
B
B
N
1
3.55
0.50
120.30
123.85
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
159
159
159
N
1
A
A
CD
OE2
GLU
GLU
153
153
0.072
0.011
1.252
1.324
N
1
A
A
CD
OE2
GLU
GLU
161
161
0.067
0.011
1.252
1.319
N
1
A
A
CD
OE2
GLU
GLU
204
204
0.068
0.011
1.252
1.320
N
1
A
A
O
O
HOH
HOH
446
446
1.55
1_555
6_555
1
A
VAL
101
-37.76
146.40
1
A
ASP
148
-66.80
1.84
1
A
CYS
196
-171.68
-177.40
1
A
SER
212
-118.99
74.42
0.263
0.188
0.194
0.188
1.8
30.
1347
13182
13182
100
random 10%
1
THROUGHOUT
0.
0.
MIR
Engh & Huber
1.8
30.
174
1110
4
0
932
0.011
2.47
0.005
1.8
30.
1P90
24908
24908
0.
0.
0.057
1
43.7
7.2
100
0.346
1.8
1.86
5.6
2531
5.1
100
data collection
HKL-2000
data scaling
SCALEPACK
phasing
SOLVE
refinement
TNT
data reduction
HKL-2000
The Three-dimensional Structure of the Core Domain of NafY from Azotobacter vinelandii determined at 1.8 resolution
1
N
N
2
N
N
3
N
N
A
LEU
147
A
LEU
49
HELX_P
A
ALA
152
A
ALA
54
5
1
6
A
ASP
154
A
ASP
56
HELX_P
A
ILE
163
A
ILE
65
1
2
10
A
GLY
175
A
GLY
77
HELX_P
A
ALA
185
A
ALA
87
1
3
11
A
ALA
198
A
ALA
100
HELX_P
A
GLY
211
A
GLY
113
1
4
14
A
PRO
214
A
PRO
116
HELX_P
A
VAL
221
A
VAL
123
1
5
8
PROTEIN BINDING
Ribonuclease H motif, PROTEIN BINDING
Q9F5X9_AZOVI
UNP
1
99
Q9F5X9
ERVPEGSIRVAIASNNGEQLDGHFGSCLRFLVYQVSAKDASLVDIRSTLDVALAEDKNAWRVEQIQDCQVLYVVSIGGPA
AAKVVRAGIHPLKKPKGCAAQEAIAELQTVMAGSPPPWLAKLVGVSAEERVRFSVSDDEDEAARA
99
243
1P90
99
243
Q9F5X9
A
1
1
145
5
2
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
A
ALA
138
A
ALA
40
A
SER
145
A
SER
47
A
ARG
127
A
ARG
29
A
SER
134
A
SER
36
A
SER
105
A
SER
7
A
SER
112
A
SER
14
A
VAL
168
A
VAL
70
A
VAL
171
A
VAL
73
A
HIS
188
A
HIS
90
A
LYS
191
A
LYS
93
A
GLN
117
A
GLN
19
A
LEU
118
A
LEU
20
A
CYS
196
A
CYS
98
A
ALA
197
A
ALA
99
BINDING SITE FOR RESIDUE EDO A 300
A
EDO
300
Software
5
A
SER
105
A
SER
7
5
1_555
A
GLN
132
A
GLN
34
5
1_555
A
ASP
137
A
ASP
39
5
1_555
A
ALA
138
A
ALA
40
5
1_555
A
SER
139
A
SER
41
5
1_555
154
P 32 2 1