0.017324
0.000000
0.000000
0.000000
0.012492
0.000000
0.000000
0.000000
0.005906
0.00000
0.00000
0.00000
Golan, G.
Zharkov, D.O.
Feinberg, H.
Fernandes, A.S.
Zaika, E.I.
Kycia, J.H.
Grollman, A.P.
Shoham, G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
57.722
80.051
169.311
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
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
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
Zn 2
65.409
ZINC ION
non-polymer
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
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
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
C
N
138
N
O
N
139
N
C
N
140
N
O
N
141
N
C
N
142
N
O
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
N
N
152
S
C
N
153
N
C
N
154
N
O
N
155
N
C
Y
156
N
C
Y
157
N
N
Y
158
N
C
Y
159
N
C
Y
160
N
N
N
161
N
O
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
172
N
O
N
173
N
H
N
174
N
H
N
175
N
N
N
176
S
C
N
177
N
C
N
178
N
O
N
179
S
C
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
O
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
H
N
195
N
H
N
196
N
H
N
197
N
N
N
198
S
C
N
199
N
C
N
200
N
O
N
201
N
C
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
O
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
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
N
C
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
N
N
228
N
O
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
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
N
249
N
C
N
250
N
S
N
251
N
C
N
252
N
O
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
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
MG
N
265
N
N
N
266
S
C
N
267
N
C
N
268
N
O
N
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
N
276
N
O
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
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
O
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
O
N
311
N
O
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
N
N
320
S
C
N
321
N
C
N
322
N
O
N
323
R
C
N
324
N
O
N
325
N
C
N
326
N
O
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
N
Y
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
N
350
N
O
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
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
Y
373
N
C
N
374
N
O
N
375
N
O
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
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
N
N
388
S
C
N
389
N
C
N
390
N
O
N
391
N
C
N
392
N
C
N
393
N
C
N
394
N
O
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
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
ZN
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
doub
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
doub
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
doub
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
doub
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
doub
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
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
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
Y
153
N
sing
Y
154
N
doub
Y
155
N
doub
N
156
N
sing
Y
157
N
sing
N
158
N
sing
Y
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
doub
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
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
doub
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
N
211
N
sing
N
212
N
sing
N
213
N
doub
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
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
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
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
Y
261
N
doub
Y
262
N
sing
Y
263
N
sing
N
264
N
sing
Y
265
N
doub
N
266
N
sing
Y
267
N
doub
N
268
N
sing
Y
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
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
doub
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
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
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
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
doub
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
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
doub
N
326
N
sing
N
327
N
sing
N
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
doub
Y
335
N
sing
Y
336
N
sing
N
337
N
sing
Y
338
N
sing
Y
339
N
doub
N
340
N
sing
Y
341
N
doub
N
342
N
sing
Y
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
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
doub
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
Y
358
N
doub
Y
359
N
sing
Y
360
N
sing
N
361
N
sing
Y
362
N
doub
N
363
N
sing
Y
364
N
doub
N
365
N
sing
Y
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
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
doub
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
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
33
5006
5016
10.1093/nar/gki796
16145054
Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.
2005
10.2210/pdb1q3b/pdb
pdb_00001q3b
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2001-12-22
MAR CCD 165 mm
SINGLE WAVELENGTH
M
x-ray
1
1.102
1.0
5ID-B
APS
1.102
SYNCHROTRON
APS BEAMLINE 5ID-B
29728.877
Endonuclease VIII
3.2.2.-
R252A
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
133
nat
water
no
no
PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTG
EEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQ
AFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERC
GSIIEKTTLSSAPFYWCPGCQH
PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTG
EEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQ
AFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERC
GSIIEKTTLSSAPFYWCPGCQH
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
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
Escherichia
Escherichia
sample
NEI
562
Escherichia coli
562
Escherichia coli
B834(DE3)
PLASMID
PET13A
1
3.29
62.59
VAPOR DIFFUSION, HANGING DROP
8.4
35% PEG 400, 0.1M Tris-HCl pH 8.4, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
288
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Database references
Derived calculations
Data collection
Refinement description
1
0
2004-08-03
1
1
2008-04-29
1
2
2011-07-13
1
3
2021-10-27
1
4
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_symmetry
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structure of the DNA repair enzyme
endonuclease-VIII (Nei) from E. coli:
The WT enzyme at 2.8 resolution.
Crystal structure of the DNA repair enzyme
endonuclease-VIII (Nei) from E. coli:
The E2A mutant at 2.3 resolution.
SEQUENCE
SEQUENCING AND CRYSTALLOGRAPHY CONFIRM THE
SEQUENCE AS THR A 34 AND ARG A 112.
RCSB
Y
RCSB
2003-07-29
REL
ZN
ZINC ION
MG
MAGNESIUM ION
GOL
GLYCEROL
HOH
water
1K3W
The Protein chain from PDB code 1K3W
PDB
experimental model
ZN2
301
2
ZN
ZN
301
A
MG2
302
3
MG
MG
302
A
MG2
303
3
MG
MG
303
A
GOL
351
4
GOL
GOL
351
A
WAT
401
5
HOH
HOH
401
A
WAT
402
5
HOH
HOH
402
A
WAT
403
5
HOH
HOH
403
A
WAT
404
5
HOH
HOH
404
A
WAT
405
5
HOH
HOH
405
A
WAT
406
5
HOH
HOH
406
A
WAT
407
5
HOH
HOH
407
A
WAT
408
5
HOH
HOH
408
A
WAT
409
5
HOH
HOH
409
A
WAT
410
5
HOH
HOH
410
A
WAT
411
5
HOH
HOH
411
A
WAT
412
5
HOH
HOH
412
A
WAT
413
5
HOH
HOH
413
A
WAT
414
5
HOH
HOH
414
A
WAT
415
5
HOH
HOH
415
A
WAT
416
5
HOH
HOH
416
A
WAT
417
5
HOH
HOH
417
A
WAT
418
5
HOH
HOH
418
A
WAT
419
5
HOH
HOH
419
A
WAT
420
5
HOH
HOH
420
A
WAT
421
5
HOH
HOH
421
A
WAT
422
5
HOH
HOH
422
A
WAT
423
5
HOH
HOH
423
A
WAT
424
5
HOH
HOH
424
A
WAT
425
5
HOH
HOH
425
A
WAT
426
5
HOH
HOH
426
A
WAT
427
5
HOH
HOH
427
A
WAT
428
5
HOH
HOH
428
A
WAT
429
5
HOH
HOH
429
A
WAT
430
5
HOH
HOH
430
A
WAT
431
5
HOH
HOH
431
A
WAT
432
5
HOH
HOH
432
A
WAT
433
5
HOH
HOH
433
A
WAT
434
5
HOH
HOH
434
A
WAT
435
5
HOH
HOH
435
A
WAT
436
5
HOH
HOH
436
A
WAT
437
5
HOH
HOH
437
A
WAT
438
5
HOH
HOH
438
A
WAT
439
5
HOH
HOH
439
A
WAT
440
5
HOH
HOH
440
A
WAT
441
5
HOH
HOH
441
A
WAT
442
5
HOH
HOH
442
A
WAT
443
5
HOH
HOH
443
A
WAT
444
5
HOH
HOH
444
A
WAT
445
5
HOH
HOH
445
A
WAT
446
5
HOH
HOH
446
A
WAT
447
5
HOH
HOH
447
A
WAT
449
5
HOH
HOH
449
A
WAT
450
5
HOH
HOH
450
A
WAT
451
5
HOH
HOH
451
A
WAT
452
5
HOH
HOH
452
A
WAT
453
5
HOH
HOH
453
A
WAT
454
5
HOH
HOH
454
A
WAT
455
5
HOH
HOH
455
A
WAT
456
5
HOH
HOH
456
A
WAT
457
5
HOH
HOH
457
A
WAT
458
5
HOH
HOH
458
A
WAT
459
5
HOH
HOH
459
A
WAT
460
5
HOH
HOH
460
A
WAT
461
5
HOH
HOH
461
A
WAT
462
5
HOH
HOH
462
A
WAT
463
5
HOH
HOH
463
A
WAT
464
5
HOH
HOH
464
A
WAT
465
5
HOH
HOH
465
A
WAT
468
5
HOH
HOH
468
A
WAT
469
5
HOH
HOH
469
A
WAT
470
5
HOH
HOH
470
A
WAT
471
5
HOH
HOH
471
A
WAT
472
5
HOH
HOH
472
A
WAT
473
5
HOH
HOH
473
A
WAT
474
5
HOH
HOH
474
A
WAT
475
5
HOH
HOH
475
A
WAT
476
5
HOH
HOH
476
A
WAT
477
5
HOH
HOH
477
A
WAT
478
5
HOH
HOH
478
A
WAT
479
5
HOH
HOH
479
A
WAT
480
5
HOH
HOH
480
A
WAT
481
5
HOH
HOH
481
A
WAT
482
5
HOH
HOH
482
A
WAT
483
5
HOH
HOH
483
A
WAT
484
5
HOH
HOH
484
A
WAT
485
5
HOH
HOH
485
A
WAT
487
5
HOH
HOH
487
A
WAT
488
5
HOH
HOH
488
A
WAT
489
5
HOH
HOH
489
A
WAT
491
5
HOH
HOH
491
A
WAT
492
5
HOH
HOH
492
A
WAT
493
5
HOH
HOH
493
A
WAT
494
5
HOH
HOH
494
A
WAT
495
5
HOH
HOH
495
A
WAT
497
5
HOH
HOH
497
A
WAT
498
5
HOH
HOH
498
A
WAT
499
5
HOH
HOH
499
A
WAT
500
5
HOH
HOH
500
A
WAT
501
5
HOH
HOH
501
A
WAT
502
5
HOH
HOH
502
A
WAT
503
5
HOH
HOH
503
A
WAT
504
5
HOH
HOH
504
A
WAT
506
5
HOH
HOH
506
A
WAT
507
5
HOH
HOH
507
A
WAT
508
5
HOH
HOH
508
A
WAT
509
5
HOH
HOH
509
A
WAT
510
5
HOH
HOH
510
A
WAT
511
5
HOH
HOH
511
A
WAT
512
5
HOH
HOH
512
A
WAT
513
5
HOH
HOH
513
A
WAT
514
5
HOH
HOH
514
A
WAT
515
5
HOH
HOH
515
A
WAT
516
5
HOH
HOH
516
A
WAT
517
5
HOH
HOH
517
A
WAT
518
5
HOH
HOH
518
A
WAT
519
5
HOH
HOH
519
A
WAT
520
5
HOH
HOH
520
A
WAT
521
5
HOH
HOH
521
A
WAT
522
5
HOH
HOH
522
A
WAT
523
5
HOH
HOH
523
A
WAT
524
5
HOH
HOH
524
A
WAT
525
5
HOH
HOH
525
A
WAT
526
5
HOH
HOH
526
A
WAT
528
5
HOH
HOH
528
A
WAT
529
5
HOH
HOH
529
A
WAT
530
5
HOH
HOH
530
A
WAT
531
5
HOH
HOH
531
A
WAT
532
5
HOH
HOH
532
A
WAT
533
5
HOH
HOH
533
A
WAT
535
5
HOH
HOH
535
A
WAT
536
5
HOH
HOH
536
A
WAT
537
5
HOH
HOH
537
A
WAT
538
5
HOH
HOH
538
A
WAT
539
5
HOH
HOH
539
A
WAT
540
5
HOH
HOH
540
A
WAT
541
5
HOH
HOH
541
A
WAT
542
5
HOH
HOH
542
A
PRO
1
n
1
PRO
1
A
ALA
2
n
2
GLU
2
A
GLY
3
n
3
GLY
3
A
PRO
4
n
4
PRO
4
A
GLU
5
n
5
GLU
5
A
ALA
6
n
6
ILE
6
A
ARG
7
n
7
ARG
7
A
ARG
8
n
8
ARG
8
A
ALA
9
n
9
ALA
9
A
ALA
10
n
10
ALA
10
A
ASP
11
n
11
ASP
11
A
ASN
12
n
12
ASN
12
A
LEU
13
n
13
LEU
13
A
GLU
14
n
14
GLU
14
A
ALA
15
n
15
ALA
15
A
ALA
16
n
16
ALA
16
A
ILE
17
n
17
ILE
17
A
LYS
18
n
18
LYS
18
A
GLY
19
n
19
GLY
19
A
LYS
20
n
20
LYS
20
A
PRO
21
n
21
PRO
21
A
LEU
22
n
22
LEU
22
A
THR
23
n
23
THR
23
A
ASP
24
n
24
ASP
24
A
VAL
25
n
25
VAL
25
A
TRP
26
n
26
TRP
26
A
PHE
27
n
27
PHE
27
A
ALA
28
n
28
ALA
28
A
PHE
29
n
29
PHE
29
A
PRO
30
n
30
PRO
30
A
GLN
31
n
31
GLN
31
A
LEU
32
n
32
LEU
32
A
LYS
33
n
33
LYS
33
A
THR
34
n
34
THR
34
A
TYR
35
n
35
TYR
35
A
GLN
36
n
36
GLN
36
A
SER
37
n
37
SER
37
A
GLN
38
n
38
GLN
38
A
LEU
39
n
39
LEU
39
A
ILE
40
n
40
ILE
40
A
GLY
41
n
41
GLY
41
A
GLN
42
n
42
GLN
42
A
HIS
43
n
43
HIS
43
A
VAL
44
n
44
VAL
44
A
THR
45
n
45
THR
45
A
HIS
46
n
46
HIS
46
A
VAL
47
n
47
VAL
47
A
GLU
48
n
48
GLU
48
A
THR
49
n
49
THR
49
A
ARG
50
n
50
ARG
50
A
GLY
51
n
51
GLY
51
A
LYS
52
n
52
LYS
52
A
ALA
53
n
53
ALA
53
A
LEU
54
n
54
LEU
54
A
LEU
55
n
55
LEU
55
A
THR
56
n
56
THR
56
A
HIS
57
n
57
HIS
57
A
PHE
58
n
58
PHE
58
A
SER
59
n
59
SER
59
A
ASN
60
n
60
ASN
60
A
ASP
61
n
61
ASP
61
A
LEU
62
n
62
LEU
62
A
THR
63
n
63
THR
63
A
LEU
64
n
64
LEU
64
A
TYR
65
n
65
TYR
65
A
SER
66
n
66
SER
66
A
HIS
67
n
67
HIS
67
A
ASN
68
n
68
ASN
68
A
GLN
69
n
69
GLN
69
A
LEU
70
n
70
LEU
70
A
TYR
71
n
71
TYR
71
A
GLY
72
n
72
GLY
72
A
VAL
73
n
73
VAL
73
A
TRP
74
n
74
TRP
74
A
ARG
75
n
75
ARG
75
A
VAL
76
n
76
VAL
76
A
VAL
77
n
77
VAL
77
A
ASP
78
n
78
ASP
78
A
THR
79
n
79
THR
79
A
GLY
80
n
80
GLY
80
A
GLU
81
n
81
GLU
81
A
GLU
82
n
82
GLU
82
A
PRO
83
n
83
PRO
83
A
ALA
84
n
84
GLN
84
A
THR
85
n
85
THR
85
A
THR
86
n
86
THR
86
A
ARG
87
n
87
ARG
87
A
VAL
88
n
88
VAL
88
A
LEU
89
n
89
LEU
89
A
ARG
90
n
90
ARG
90
A
VAL
91
n
91
VAL
91
A
LYS
92
n
92
LYS
92
A
LEU
93
n
93
LEU
93
A
GLN
94
n
94
GLN
94
A
THR
95
n
95
THR
95
A
ALA
96
n
96
ALA
96
A
ASP
97
n
97
ASP
97
A
LYS
98
n
98
LYS
98
A
THR
99
n
99
THR
99
A
ILE
100
n
100
ILE
100
A
LEU
101
n
101
LEU
101
A
LEU
102
n
102
LEU
102
A
TYR
103
n
103
TYR
103
A
SER
104
n
104
SER
104
A
ALA
105
n
105
ALA
105
A
SER
106
n
106
SER
106
A
ASP
107
n
107
ASP
107
A
ILE
108
n
108
ILE
108
A
GLU
109
n
109
GLU
109
A
MET
110
n
110
MET
110
A
LEU
111
n
111
LEU
111
A
ARG
112
n
112
ARG
112
A
PRO
113
n
113
PRO
113
A
GLU
114
n
114
GLU
114
A
GLN
115
n
115
GLN
115
A
LEU
116
n
116
LEU
116
A
THR
117
n
117
THR
117
A
THR
118
n
118
THR
118
A
HIS
119
n
119
HIS
119
A
PRO
120
n
120
PRO
120
A
PHE
121
n
121
PHE
121
A
LEU
122
n
122
LEU
122
A
GLN
123
n
123
GLN
123
A
ARG
124
n
124
ARG
124
A
VAL
125
n
125
VAL
125
A
GLY
126
n
126
GLY
126
A
PRO
127
n
127
PRO
127
A
ASP
128
n
128
ASP
128
A
VAL
129
n
129
VAL
129
A
LEU
130
n
130
LEU
130
A
ASP
131
n
131
ASP
131
A
PRO
132
n
132
PRO
132
A
ASN
133
n
133
ASN
133
A
LEU
134
n
134
LEU
134
A
THR
135
n
135
THR
135
A
PRO
136
n
136
PRO
136
A
GLU
137
n
137
GLU
137
A
VAL
138
n
138
VAL
138
A
VAL
139
n
139
VAL
139
A
LYS
140
n
140
LYS
140
A
GLU
141
n
141
GLU
141
A
ARG
142
n
142
ARG
142
A
LEU
143
n
143
LEU
143
A
LEU
144
n
144
LEU
144
A
SER
145
n
145
SER
145
A
PRO
146
n
146
PRO
146
A
ARG
147
n
147
ARG
147
A
PHE
148
n
148
PHE
148
A
ARG
149
n
149
ARG
149
A
ASN
150
n
150
ASN
150
A
ARG
151
n
151
ARG
151
A
GLN
152
n
152
GLN
152
A
PHE
153
n
153
PHE
153
A
ALA
154
n
154
ALA
154
A
GLY
155
n
155
GLY
155
A
LEU
156
n
156
LEU
156
A
LEU
157
n
157
LEU
157
A
LEU
158
n
158
LEU
158
A
ASP
159
n
159
ASP
159
A
GLN
160
n
160
GLN
160
A
ALA
161
n
161
ALA
161
A
PHE
162
n
162
PHE
162
A
LEU
163
n
163
LEU
163
A
ALA
164
n
164
ALA
164
A
GLY
165
n
165
GLY
165
A
LEU
166
n
166
LEU
166
A
GLY
167
n
167
GLY
167
A
ASN
168
n
168
ASN
168
A
TYR
169
n
169
TYR
169
A
LEU
170
n
170
LEU
170
A
ARG
171
n
171
ARG
171
A
VAL
172
n
172
VAL
172
A
GLU
173
n
173
GLU
173
A
ILE
174
n
174
ILE
174
A
LEU
175
n
175
LEU
175
A
TRP
176
n
176
TRP
176
A
GLN
177
n
177
GLN
177
A
VAL
178
n
178
VAL
178
A
GLY
179
n
179
GLY
179
A
LEU
180
n
180
LEU
180
A
THR
181
n
181
THR
181
A
GLY
182
n
182
GLY
182
A
ASN
183
n
183
ASN
183
A
HIS
184
n
184
HIS
184
A
LYS
185
n
185
LYS
185
A
ALA
186
n
186
ALA
186
A
LYS
187
n
187
LYS
187
A
ASP
188
n
188
ASP
188
A
LEU
189
n
189
LEU
189
A
ASN
190
n
190
ASN
190
A
ALA
191
n
191
ALA
191
A
ALA
192
n
192
ALA
192
A
GLN
193
n
193
GLN
193
A
LEU
194
n
194
LEU
194
A
ASP
195
n
195
ASP
195
A
ALA
196
n
196
ALA
196
A
LEU
197
n
197
LEU
197
A
ALA
198
n
198
ALA
198
A
HIS
199
n
199
HIS
199
A
ALA
200
n
200
ALA
200
A
LEU
201
n
201
LEU
201
A
LEU
202
n
202
LEU
202
A
GLU
203
n
203
GLU
203
A
ILE
204
n
204
ILE
204
A
PRO
205
n
205
PRO
205
A
ARG
206
n
206
ARG
206
A
PHE
207
n
207
PHE
207
A
SER
208
n
208
SER
208
A
TYR
209
n
209
TYR
209
A
ALA
210
n
210
ALA
210
A
THR
211
n
211
THR
211
A
ARG
212
n
212
ARG
212
A
GLY
213
n
213
GLY
213
A
GLN
214
n
214
GLN
214
A
VAL
215
n
215
VAL
215
A
ASP
216
n
216
ASP
216
A
GLU
217
n
217
GLU
217
A
ASN
218
n
218
ASN
218
A
LYS
219
n
219
LYS
219
A
HIS
220
n
220
HIS
220
A
HIS
221
n
221
HIS
221
A
GLY
222
n
222
GLY
222
A
ALA
223
n
223
ALA
223
A
LEU
224
n
224
LEU
224
A
PHE
225
n
225
PHE
225
A
ARG
226
n
226
ARG
226
A
PHE
227
n
227
PHE
227
A
LYS
228
n
228
LYS
228
A
VAL
229
n
229
VAL
229
A
PHE
230
n
230
PHE
230
A
HIS
231
n
231
HIS
231
A
ARG
232
n
232
ARG
232
A
ASP
233
n
233
ASP
233
A
GLY
234
n
234
GLY
234
A
GLU
235
n
235
GLU
235
A
PRO
236
n
236
PRO
236
A
CYS
237
n
237
CYS
237
A
GLU
238
n
238
GLU
238
A
ARG
239
n
239
ARG
239
A
CYS
240
n
240
CYS
240
A
GLY
241
n
241
GLY
241
A
SER
242
n
242
SER
242
A
ILE
243
n
243
ILE
243
A
ILE
244
n
244
ILE
244
A
GLU
245
n
245
GLU
245
A
LYS
246
n
246
LYS
246
A
THR
247
n
247
THR
247
A
THR
248
n
248
THR
248
A
ALA
249
n
249
LEU
249
A
n
250
250
A
n
251
251
A
n
252
252
A
PRO
253
n
253
PRO
253
A
PHE
254
n
254
PHE
254
A
TYR
255
n
255
TYR
255
A
TRP
256
n
256
TRP
256
A
CYS
257
n
257
CYS
257
A
PRO
258
n
258
PRO
258
A
GLY
259
n
259
GLY
259
A
CYS
260
n
260
CYS
260
A
GLN
261
n
261
GLN
261
A
HIS
262
n
262
HIS
262
A
author_defined_assembly
1
monomeric
A
HIS
184
A
NE2
HIS
184
1_555
A
MG
302
C
MG
MG
1_555
A
HIS
262
A
O
HIS
262
1_555
116.6
A
HIS
184
A
NE2
HIS
184
1_555
A
MG
302
C
MG
MG
1_555
A
HIS
262
A
OXT
HIS
262
1_555
97.1
A
HIS
262
A
O
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
A
HIS
262
A
OXT
HIS
262
1_555
49.1
A
HIS
184
A
NE2
HIS
184
1_555
A
MG
302
C
MG
MG
1_555
A
HIS
262
A
NE2
HIS
262
3_555
118.4
A
HIS
262
A
O
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
A
HIS
262
A
NE2
HIS
262
3_555
99.6
A
HIS
262
A
OXT
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
A
HIS
262
A
NE2
HIS
262
3_555
70.4
A
HIS
184
A
NE2
HIS
184
1_555
A
MG
302
C
MG
MG
1_555
A
HOH
530
F
O
HOH
1_555
96.0
A
HIS
262
A
O
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
A
HOH
530
F
O
HOH
1_555
107.3
A
HIS
262
A
OXT
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
A
HOH
530
F
O
HOH
1_555
156.4
A
HIS
262
A
NE2
HIS
262
3_555
A
MG
302
C
MG
MG
1_555
A
HOH
530
F
O
HOH
1_555
119.5
A
ASP
195
A
OD1
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
ASP
195
A
OD2
ASP
195
2_555
49.1
A
ASP
195
A
OD1
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
HIS
199
A
NE2
HIS
199
2_555
115.2
A
ASP
195
A
OD2
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
HIS
199
A
NE2
HIS
199
2_555
85.7
A
ASP
195
A
OD1
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
HIS
220
A
NE2
HIS
220
1_555
111.1
A
ASP
195
A
OD2
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
HIS
220
A
NE2
HIS
220
1_555
93.0
A
HIS
199
A
NE2
HIS
199
2_555
A
MG
303
D
MG
MG
1_555
A
HIS
220
A
NE2
HIS
220
1_555
115.6
A
ASP
195
A
OD1
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
HOH
468
F
O
HOH
1_555
98.1
A
ASP
195
A
OD2
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
A
HOH
468
F
O
HOH
1_555
147.2
A
HIS
199
A
NE2
HIS
199
2_555
A
MG
303
D
MG
MG
1_555
A
HOH
468
F
O
HOH
1_555
112.2
A
HIS
220
A
NE2
HIS
220
1_555
A
MG
303
D
MG
MG
1_555
A
HOH
468
F
O
HOH
1_555
102.5
A
CYS
237
A
SG
CYS
237
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
240
A
SG
CYS
240
1_555
113.9
A
CYS
237
A
SG
CYS
237
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
257
A
SG
CYS
257
1_555
107.9
A
CYS
240
A
SG
CYS
240
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
257
A
SG
CYS
257
1_555
93.2
A
CYS
237
A
SG
CYS
237
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
260
A
SG
CYS
260
1_555
105.9
A
CYS
240
A
SG
CYS
240
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
260
A
SG
CYS
260
1_555
118.2
A
CYS
257
A
SG
CYS
257
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
260
A
SG
CYS
260
1_555
117.3
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
N
ASP
24
A
N
ASP
24
A
O
GLN
94
A
O
GLN
94
A
N
VAL
91
A
N
VAL
91
A
O
LEU
102
A
O
LEU
102
A
O
THR
99
A
O
THR
99
A
N
VAL
77
A
N
VAL
77
A
N
GLU
48
A
N
GLU
48
A
O
LEU
55
A
O
LEU
55
A
N
THR
56
A
N
THR
56
A
O
LEU
64
A
O
LEU
64
A
N
THR
63
A
N
THR
63
A
O
LEU
111
A
O
LEU
111
A
N
GLU
245
A
N
GLU
245
A
O
TRP
256
A
O
TRP
256
1
A
CG
GLU
2
A
CG
GLU
2
1
Y
1
A
CD
GLU
2
A
CD
GLU
2
1
Y
1
A
OE1
GLU
2
A
OE1
GLU
2
1
Y
1
A
OE2
GLU
2
A
OE2
GLU
2
1
Y
1
A
CG1
ILE
6
A
CG1
ILE
6
1
Y
1
A
CG2
ILE
6
A
CG2
ILE
6
1
Y
1
A
CD1
ILE
6
A
CD1
ILE
6
1
Y
1
A
CG
GLN
84
A
CG
GLN
84
1
Y
1
A
CD
GLN
84
A
CD
GLN
84
1
Y
1
A
OE1
GLN
84
A
OE1
GLN
84
1
Y
1
A
NE2
GLN
84
A
NE2
GLN
84
1
Y
1
A
CG
LEU
249
A
CG
LEU
249
1
Y
1
A
CD1
LEU
249
A
CD1
LEU
249
1
Y
1
A
CD2
LEU
249
A
CD2
LEU
249
1
Y
1
A
SER
250
A
SER
250
1
Y
1
A
SER
251
A
SER
251
1
Y
1
A
ALA
252
A
ALA
252
1
Y
1
A
A
O
O
HOH
HOH
530
530
1.94
1_555
3_555
1
A
A
O
O
HOH
HOH
518
518
2.05
1_555
3_555
1
A
GLU
2
-164.47
3.73
1
A
GLU
5
-29.96
-57.59
1
A
ASP
61
80.60
-4.02
1
A
GLN
69
53.24
-126.78
1
A
SER
104
62.99
-33.66
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
GOL.PAR
GOL.TOP
45.3
-13.87
0.00
0.00
22.45
0.00
-8.58
0.26
0.006
0.228
0.228
2.05
29.21
2095
25032
25024
8.4
99.7
RANDOM
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
The Protein chain from PDB code 1K3W
FLAT MODEL
59.3061
0.357914
0.33
0.29
5.00
0.42
0.42
2.05
29.21
133
2210
9
0
2068
0.006
1.2
23.7
0.79
1.37
1.50
2.19
2.00
2.04
2.00
3.03
2.50
0.376
0.021
0.371
2.18
317
3770
6
7.8
99.6
25.9
2.05
30
1Q3B
25032
25032
0
0
0.06
1
5.43
99.9
0.421
2.05
2.09
1220
1
5
100.0
refinement
CNS
1.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution.
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
A
GLY
3
A
GLY
3
HELX_P
A
LYS
18
A
LYS
18
1
1
16
A
PHE
29
A
PHE
29
HELX_P
A
THR
34
A
THR
34
5
2
6
A
TYR
35
A
TYR
35
HELX_P
A
ILE
40
A
ILE
40
1
3
6
A
ARG
112
A
ARG
112
HELX_P
A
THR
117
A
THR
117
1
4
6
A
HIS
119
A
HIS
119
HELX_P
A
VAL
125
A
VAL
125
1
5
7
A
THR
135
A
THR
135
HELX_P
A
SER
145
A
SER
145
1
6
11
A
GLN
152
A
GLN
152
HELX_P
A
LEU
157
A
LEU
157
1
7
6
A
GLY
167
A
GLY
167
HELX_P
A
VAL
178
A
VAL
178
1
8
12
A
LYS
185
A
LYS
185
HELX_P
A
LEU
189
A
LEU
189
5
9
5
A
ASN
190
A
ASN
190
HELX_P
A
ARG
212
A
ARG
212
1
10
23
A
ASP
216
A
ASP
216
HELX_P
A
HIS
220
A
HIS
220
5
11
5
metalc
2.387
A
HIS
184
A
NE2
HIS
184
1_555
A
MG
302
C
MG
MG
1_555
metalc
1.836
A
ASP
195
A
OD1
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
metalc
2.913
A
ASP
195
A
OD2
ASP
195
2_555
A
MG
303
D
MG
MG
1_555
metalc
1.918
A
HIS
199
A
NE2
HIS
199
2_555
A
MG
303
D
MG
MG
1_555
metalc
2.017
A
HIS
220
A
NE2
HIS
220
1_555
A
MG
303
D
MG
MG
1_555
metalc
2.333
A
CYS
237
A
SG
CYS
237
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.380
A
CYS
240
A
SG
CYS
240
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.277
A
CYS
257
A
SG
CYS
257
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.276
A
CYS
260
A
SG
CYS
260
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
1.913
A
HIS
262
A
O
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
metalc
2.917
A
HIS
262
A
OXT
HIS
262
1_555
A
MG
302
C
MG
MG
1_555
metalc
2.277
A
HIS
262
A
NE2
HIS
262
3_555
A
MG
302
C
MG
MG
1_555
metalc
2.267
A
MG
302
C
MG
MG
1_555
A
HOH
530
F
O
HOH
1_555
metalc
2.322
A
MG
303
D
MG
MG
1_555
A
HOH
468
F
O
HOH
1_555
HYDROLASE
hydrolase
END8_ECOLI
UNP
1
1
P50465
PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTG
EEPQTTRVLRVKLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQ
AFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERC
GSIIEKTTLSSRPFYWCPGCQH
1
262
1Q3B
1
262
P50465
A
1
1
262
1
PRO
SEE REMARK 999
THR
34
1Q3B
A
P50465
UNP
34
34
1
THR
SEE REMARK 999
ARG
112
1Q3B
A
P50465
UNP
112
112
1
ARG
engineered mutation
ALA
252
1Q3B
A
P50465
UNP
252
252
4
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ASP
24
A
ASP
24
A
PHE
27
A
PHE
27
A
LEU
89
A
LEU
89
A
GLN
94
A
GLN
94
A
LYS
98
A
LYS
98
A
TYR
103
A
TYR
103
A
VAL
73
A
VAL
73
A
ASP
78
A
ASP
78
A
VAL
44
A
VAL
44
A
ARG
50
A
ARG
50
A
ALA
53
A
ALA
53
A
PHE
58
A
PHE
58
A
THR
63
A
THR
63
A
HIS
67
A
HIS
67
A
ASP
107
A
ASP
107
A
LEU
111
A
LEU
111
A
GLU
245
A
GLU
245
A
LYS
246
A
LYS
246
A
TYR
255
A
TYR
255
A
TRP
256
A
TRP
256
BINDING SITE FOR RESIDUE ZN A 301
A
ZN
301
Software
4
BINDING SITE FOR RESIDUE MG A 302
A
MG
302
Software
4
BINDING SITE FOR RESIDUE MG A 303
A
MG
303
Software
4
BINDING SITE FOR RESIDUE GOL A 351
A
GOL
351
Software
3
A
CYS
237
A
CYS
237
4
1_555
A
CYS
240
A
CYS
240
4
1_555
A
CYS
257
A
CYS
257
4
1_555
A
CYS
260
A
CYS
260
4
1_555
A
HIS
184
A
HIS
184
4
1_555
A
HIS
262
A
HIS
262
4
3_555
A
HIS
262
A
HIS
262
4
1_555
A
HOH
530
F
HOH
4
1_555
A
ASP
195
A
ASP
195
4
2_555
A
HIS
199
A
HIS
199
4
2_555
A
HIS
220
A
HIS
220
4
1_555
A
HOH
468
F
HOH
4
1_555
A
ASN
12
A
ASN
12
3
1_555
A
VAL
76
A
VAL
76
3
1_555
A
HOH
526
F
HOH
3
1_555
23
I 2 2 2