0.012545
0.000000
0.011336
0.000000
0.018657
0.000000
0.000000
0.000000
0.020504
0.000000
0.000000
0.000000
Ho, K.L.
McNae, I.W.
Schmiedeberg, L.
Klose, R.J.
Bird, A.P.
Walkinshaw, M.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
132.100
90.000
79.710
53.600
65.730
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
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
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
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 Se
196.106
n
SELENOMETHIONINE
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
US
Mol.Cell
MOCEFL
2168
1097-2765
29
525
531
10.1016/j.molcel.2007.12.028
18313390
MeCP2 binding to DNA depends upon hydration at methyl-CpG
2008
10.2210/pdb3c2i/pdb
pdb_00003c2i
100
1
mirrors
CCD
2006-08-07
MARMOSAIC 225 mm CCD
silicon
SINGLE WAVELENGTH
M
x-ray
1
0.97800
1.0
BM14
ESRF
0.97800
SYNCHROTRON
ESRF BEAMLINE BM14
11281.381
Methyl-CpG-binding protein 2
UNP residues 77-167, Human MeCP2 MBD domain
A140(MSE)
1
man
polymer
6138.003
DNA (5'-D(*DTP*DCP*DTP*DGP*DGP*DAP*DAP*(5CM)P*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DTP*DA)-3')
1
syn
polymer
6156.032
DNA (5'-D(*DAP*DTP*DAP*DGP*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*(5CM)P*DGP*DTP*DTP*DCP*DCP*DAP*DG)-3')
1
syn
polymer
18.015
water
47
nat
water
MeCP-2 protein, MeCP2
no
yes
ASASPKQRRSIIRDRGP(MSE)YDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELI(MSE)YFEKVGDT
SLDPNDFDFTVTGRGSPSRHHHHHH
ASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDTSLDPNDFD
FTVTGRGSPSRHHHHHH
A
polypeptide(L)
no
yes
(DT)(DC)(DT)(DG)(DG)(DA)(DA)(5CM)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT)(DT)(DC)(DT)
(DA)
TCTGGAACGGAATTCTTCTA
B
polydeoxyribonucleotide
no
yes
(DA)(DT)(DA)(DG)(DA)(DA)(DG)(DA)(DA)(DT)(DT)(DC)(5CM)(DG)(DT)(DT)(DC)(DC)(DA)
(DG)
ATAGAAGAATTCCGTTCCAG
C
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
sample
MECP2
9606
Homo sapiens
562
Escherichia coli
BL21(DE3)pLys
plasmid
pET30b
1
2.21
44.33
VAPOR DIFFUSION, HANGING DROP
6.5
26% PEG2000, 0.2M Ammonium acetate, 0.01M Mg acetate, 0.05M Na cacodylate pH6.5, 0.002M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K
290
PEG2000
1
Ammonium acetate
1
Mg acetate
1
Na cacodylate
1
HOH
1
PEG2000
2
Ammonium acetate
2
Mg acetate
2
Na cacodylate
2
HOH
2
-13.134
1
19
B
2
C
40
-1.661
B_DC2:DG40_C
1
-5.465
-0.081
0.119
-0.184
-1.291
1
20
B
3
C
39
1.832
B_DT3:DA39_C
2
-3.289
-0.230
0.051
-0.375
9.161
1
19
B
4
C
38
5.688
B_DG4:DC38_C
3
-7.591
-0.436
0.155
-0.190
6.212
1
19
B
5
C
37
0.412
B_DG5:DC37_C
4
-10.624
-0.700
-0.017
-0.416
-4.051
1
20
B
6
C
36
-0.170
B_DA6:DT36_C
5
-9.789
0.266
0.052
-0.354
-5.756
1
20
B
7
C
35
-0.979
B_DA7:DT35_C
6
-8.833
-0.077
0.328
-0.227
-8.530
1
19
B
8
C
34
-3.419
B_5CM8:DG34_C
7
-4.548
0.318
0.101
-0.283
-9.472
1
19
B
9
C
33
1.665
B_DG9:5CM33_C
8
-7.544
-0.111
-0.118
-0.081
3.496
1
19
B
10
C
32
1.278
B_DG10:DC32_C
9
-2.442
-0.436
-0.005
-0.272
1.276
1
20
B
11
C
31
-2.191
B_DA11:DT31_C
10
-19.739
0.191
-0.174
-0.163
0.756
1
20
B
12
C
30
0.447
B_DA12:DT30_C
11
-14.197
-0.005
0.060
-0.322
-2.221
1
20
B
13
C
29
-2.372
B_DT13:DA29_C
12
-15.431
-0.014
0.088
-0.287
-1.905
1
20
B
14
C
28
2.355
B_DT14:DA28_C
13
-15.022
0.163
0.004
-0.095
-10.111
1
19
B
15
C
27
2.413
B_DC15:DG27_C
14
-14.195
0.131
0.357
-0.004
-6.045
1
20
B
16
C
26
-1.264
B_DT16:DA26_C
15
-10.410
-0.511
0.167
-0.241
-5.072
1
20
B
17
C
25
-2.561
B_DT17:DA25_C
16
-19.431
-0.058
-0.016
-0.502
-5.821
1
19
B
18
C
24
5.495
B_DC18:DG24_C
17
-5.351
0.963
0.086
-0.334
-11.672
1
20
B
19
C
23
7.235
B_DT19:DA23_C
18
-20.254
-0.194
0.331
0.071
-7.117
1
20
B
20
C
22
3.443
B_DA20:DT22_C
19
-8.099
0.072
-0.009
-0.272
2.998
28.983
B
B
2
3
1.839
C
C
40
39
3.030
0.920
-0.319
-0.600
BB_DC2DT3:DA39DG40_CC
1
0.955
-1.909
28.954
-1.385
0.832
3.163
34.536
B
B
3
4
5.792
C
C
39
38
3.084
3.433
0.448
0.892
BB_DT3DG4:DC38DA39_CC
2
0.624
-1.052
34.365
0.994
-0.663
3.387
33.063
B
B
4
5
7.769
C
C
38
37
3.362
4.407
-0.430
0.274
BB_DG4DG5:DC37DC38_CC
3
-1.742
3.072
32.731
-0.291
0.450
3.420
40.144
B
B
5
6
4.266
C
C
37
36
3.446
2.923
-0.209
-0.331
BB_DG5DA6:DT36DC37_CC
4
-2.999
4.377
39.933
-0.833
-0.055
3.306
36.835
B
B
6
7
-4.772
C
C
36
35
3.254
-3.010
-0.429
-0.541
BB_DA6DA7:DT35DT36_CC
5
-2.320
3.677
36.645
-0.445
0.362
3.444
37.445
B
B
7
8
-5.399
C
C
35
34
3.409
-3.460
-0.224
-0.749
BB_DA75CM8:DG34DT35_CC
6
2.189
-3.417
37.228
-0.690
0.650
3.397
42.300
B
B
8
9
1.990
C
C
34
33
3.373
1.435
0.270
0.516
BB_5CM8DG9:5CM33DG34_CC
7
2.009
-2.786
42.231
0.563
-0.161
2.996
27.565
B
B
9
10
6.500
C
C
33
32
2.975
3.090
0.581
0.538
BB_DG9DG10:DC325CM33_CC
8
-0.907
1.908
27.380
0.439
-1.422
3.536
40.393
B
B
10
11
3.367
C
C
32
31
3.425
2.323
-1.474
1.054
BB_DG10DA11:DT31DC32_CC
9
-1.736
2.517
40.293
1.248
1.927
3.149
38.162
B
B
11
12
-5.578
C
C
31
30
3.158
-3.642
0.323
-0.072
BB_DA11DA12:DT30DT31_CC
10
-0.286
0.438
37.993
0.334
-0.530
3.377
32.413
B
B
12
13
-2.326
C
C
30
29
3.356
-1.298
0.168
-0.501
BB_DA12DT13:DA29DT30_CC
11
0.807
-1.447
32.378
-0.662
-0.155
3.151
35.701
B
B
13
14
-0.560
C
C
29
28
3.145
-0.343
0.094
-0.495
BB_DT13DT14:DA28DA29_CC
12
1.276
-2.083
35.677
-0.760
0.024
3.498
39.305
B
B
14
15
-1.260
C
C
28
27
3.493
-0.847
-0.025
-0.432
BB_DT14DC15:DG27DA28_CC
13
-1.933
2.875
39.251
-0.535
-0.209
3.269
28.699
B
B
15
16
-3.767
C
C
27
26
3.239
-1.865
-0.654
-0.125
BB_DC15DT16:DA26DG27_CC
14
-1.469
2.968
28.602
0.166
0.990
3.077
41.852
B
B
16
17
-6.024
C
C
26
25
3.166
-4.295
0.004
0.735
BB_DT16DT17:DA25DA26_CC
15
1.512
-2.121
41.614
1.459
0.146
3.356
42.698
B
B
17
18
-2.888
C
C
25
24
3.394
-2.102
0.910
1.113
BB_DT17DC18:DG24DA25_CC
16
0.931
-1.279
42.639
1.747
-1.153
3.459
29.770
B
B
18
19
-1.405
C
C
24
23
3.448
-0.722
-0.887
0.798
BB_DC18DT19:DA23DG24_CC
17
-1.161
2.260
29.739
1.713
1.470
3.189
45.727
B
B
19
20
-2.851
C
C
23
22
3.224
-2.213
0.917
1.763
BB_DT19DA20:DT22DA23_CC
18
2.931
-3.776
45.587
2.458
-0.930
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Other
Database references
Derived calculations
1
0
2008-05-13
1
1
2011-07-13
1
2
2017-01-11
1
3
2021-11-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_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.ptnr2_auth_asym_id
_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_ref_seq_dif.details
RCSB
Y
PDBJ
2008-01-25
REL
REL
HOH
water
synthetic oligonucleotide
sample
synthetic oligonucleotide
sample
HOH
3
4
HOH
HOH
176
A
HOH
5
4
HOH
HOH
177
A
HOH
6
4
HOH
HOH
178
A
HOH
9
4
HOH
HOH
179
A
HOH
12
4
HOH
HOH
180
A
HOH
20
4
HOH
HOH
181
A
HOH
21
4
HOH
HOH
182
A
HOH
22
4
HOH
HOH
183
A
HOH
23
4
HOH
HOH
184
A
HOH
28
4
HOH
HOH
185
A
HOH
33
4
HOH
HOH
186
A
HOH
34
4
HOH
HOH
187
A
HOH
37
4
HOH
HOH
188
A
HOH
40
4
HOH
HOH
189
A
HOH
41
4
HOH
HOH
190
A
HOH
43
4
HOH
HOH
191
A
HOH
45
4
HOH
HOH
192
A
HOH
1
4
HOH
HOH
21
B
HOH
4
4
HOH
HOH
22
B
HOH
13
4
HOH
HOH
23
B
HOH
14
4
HOH
HOH
24
B
HOH
15
4
HOH
HOH
25
B
HOH
17
4
HOH
HOH
26
B
HOH
18
4
HOH
HOH
27
B
HOH
11
4
HOH
HOH
29
B
HOH
7
4
HOH
HOH
30
B
HOH
30
4
HOH
HOH
31
B
HOH
24
4
HOH
HOH
32
B
HOH
46
4
HOH
HOH
33
B
HOH
19
4
HOH
HOH
174
B
HOH
47
4
HOH
HOH
175
B
HOH
2
4
HOH
HOH
41
C
HOH
8
4
HOH
HOH
42
C
HOH
10
4
HOH
HOH
43
C
HOH
16
4
HOH
HOH
44
C
HOH
39
4
HOH
HOH
45
C
HOH
25
4
HOH
HOH
46
C
HOH
26
4
HOH
HOH
47
C
HOH
27
4
HOH
HOH
48
C
HOH
29
4
HOH
HOH
49
C
HOH
31
4
HOH
HOH
50
C
HOH
32
4
HOH
HOH
51
C
HOH
35
4
HOH
HOH
52
C
HOH
36
4
HOH
HOH
53
C
HOH
38
4
HOH
HOH
54
C
HOH
42
4
HOH
HOH
55
C
HOH
44
4
HOH
HOH
56
C
Se
59.731
0.837
0.365
0.147
1.023
Se
60.000
0.971
0.024
0.052
0.861
0.440
330
0.500
590
0.450
759
0.380
905
0.290
1004
0.190
1129
0.110
1190
0.060
1208
0.530
0.530
0.550
7115
6648
467
0.940
0.950
0.870
317
261
56
0.900
0.910
0.730
972
883
89
0.840
0.850
0.760
1222
1131
91
0.640
0.650
0.540
1207
1136
71
0.300
0.300
0.270
2152
2038
114
0.140
0.140
0.150
1245
1199
46
n
1
77
A
n
2
78
A
n
3
79
A
n
4
80
A
n
5
81
A
n
6
82
A
n
7
83
A
n
8
84
A
n
9
85
A
n
10
86
A
n
11
87
A
n
12
88
A
n
13
89
A
n
14
90
A
ARG
91
n
15
ARG
91
A
GLY
92
n
16
GLY
92
A
PRO
93
n
17
PRO
93
A
MSE
94
n
18
MSE
94
A
TYR
95
n
19
TYR
95
A
ASP
96
n
20
ASP
96
A
ASP
97
n
21
ASP
97
A
PRO
98
n
22
PRO
98
A
THR
99
n
23
THR
99
A
LEU
100
n
24
LEU
100
A
PRO
101
n
25
PRO
101
A
GLU
102
n
26
GLU
102
A
GLY
103
n
27
GLY
103
A
TRP
104
n
28
TRP
104
A
THR
105
n
29
THR
105
A
ARG
106
n
30
ARG
106
A
LYS
107
n
31
LYS
107
A
LEU
108
n
32
LEU
108
A
LYS
109
n
33
LYS
109
A
GLN
110
n
34
GLN
110
A
ARG
111
n
35
ARG
111
A
LYS
112
n
36
LYS
112
A
SER
113
n
37
SER
113
A
GLY
114
n
38
GLY
114
A
ARG
115
n
39
ARG
115
A
SER
116
n
40
SER
116
A
ALA
117
n
41
ALA
117
A
GLY
118
n
42
GLY
118
A
LYS
119
n
43
LYS
119
A
TYR
120
n
44
TYR
120
A
ASP
121
n
45
ASP
121
A
VAL
122
n
46
VAL
122
A
TYR
123
n
47
TYR
123
A
LEU
124
n
48
LEU
124
A
ILE
125
n
49
ILE
125
A
ASN
126
n
50
ASN
126
A
PRO
127
n
51
PRO
127
A
GLN
128
n
52
GLN
128
A
GLY
129
n
53
GLY
129
A
LYS
130
n
54
LYS
130
A
ALA
131
n
55
ALA
131
A
PHE
132
n
56
PHE
132
A
ARG
133
n
57
ARG
133
A
SER
134
n
58
SER
134
A
LYS
135
n
59
LYS
135
A
VAL
136
n
60
VAL
136
A
GLU
137
n
61
GLU
137
A
LEU
138
n
62
LEU
138
A
ILE
139
n
63
ILE
139
A
MSE
140
n
64
MSE
140
A
TYR
141
n
65
TYR
141
A
PHE
142
n
66
PHE
142
A
GLU
143
n
67
GLU
143
A
LYS
144
n
68
LYS
144
A
VAL
145
n
69
VAL
145
A
GLY
146
n
70
GLY
146
A
ASP
147
n
71
ASP
147
A
THR
148
n
72
THR
148
A
SER
149
n
73
SER
149
A
LEU
150
n
74
LEU
150
A
ASP
151
n
75
ASP
151
A
PRO
152
n
76
PRO
152
A
ASN
153
n
77
ASN
153
A
ASP
154
n
78
ASP
154
A
PHE
155
n
79
PHE
155
A
ASP
156
n
80
ASP
156
A
PHE
157
n
81
PHE
157
A
THR
158
n
82
THR
158
A
VAL
159
n
83
VAL
159
A
THR
160
n
84
THR
160
A
GLY
161
n
85
GLY
161
A
ARG
162
n
86
ARG
162
A
n
87
163
A
n
88
164
A
n
89
165
A
n
90
166
A
n
91
167
A
n
92
168
A
n
93
169
A
n
94
170
A
n
95
171
A
n
96
172
A
n
97
173
A
DT
1
n
1
DT
1
B
DC
2
n
2
DC
2
B
DT
3
n
3
DT
3
B
DG
4
n
4
DG
4
B
DG
5
n
5
DG
5
B
DA
6
n
6
DA
6
B
DA
7
n
7
DA
7
B
5CM
8
n
8
5CM
8
B
DG
9
n
9
DG
9
B
DG
10
n
10
DG
10
B
DA
11
n
11
DA
11
B
DA
12
n
12
DA
12
B
DT
13
n
13
DT
13
B
DT
14
n
14
DT
14
B
DC
15
n
15
DC
15
B
DT
16
n
16
DT
16
B
DT
17
n
17
DT
17
B
DC
18
n
18
DC
18
B
DT
19
n
19
DT
19
B
DA
20
n
20
DA
20
B
DA
21
n
1
DA
21
C
DT
22
n
2
DT
22
C
DA
23
n
3
DA
23
C
DG
24
n
4
DG
24
C
DA
25
n
5
DA
25
C
DA
26
n
6
DA
26
C
DG
27
n
7
DG
27
C
DA
28
n
8
DA
28
C
DA
29
n
9
DA
29
C
DT
30
n
10
DT
30
C
DT
31
n
11
DT
31
C
DC
32
n
12
DC
32
C
5CM
33
n
13
5CM
33
C
DG
34
n
14
DG
34
C
DT
35
n
15
DT
35
C
DT
36
n
16
DT
36
C
DC
37
n
17
DC
37
C
DC
38
n
18
DC
38
C
DA
39
n
19
DA
39
C
DG
40
n
20
DG
40
C
author_and_software_defined_assembly
PISA
3
trimeric
4520
-12.7
10880
A
MSE
94
SELENOMETHIONINE
A
MSE
18
MET
A
MSE
140
SELENOMETHIONINE
A
MSE
64
MET
B
5CM
8
B
5CM
8
DC
C
5CM
33
C
5CM
13
DC
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
THR
105
A
N
THR
29
A
O
ILE
125
A
O
ILE
49
A
N
LEU
124
A
N
LEU
48
A
O
PHE
132
A
O
PHE
56
1
A
ALA
77
A
ALA
1
1
Y
1
A
SER
78
A
SER
2
1
Y
1
A
ALA
79
A
ALA
3
1
Y
1
A
SER
80
A
SER
4
1
Y
1
A
PRO
81
A
PRO
5
1
Y
1
A
LYS
82
A
LYS
6
1
Y
1
A
GLN
83
A
GLN
7
1
Y
1
A
ARG
84
A
ARG
8
1
Y
1
A
ARG
85
A
ARG
9
1
Y
1
A
SER
86
A
SER
10
1
Y
1
A
ILE
87
A
ILE
11
1
Y
1
A
ILE
88
A
ILE
12
1
Y
1
A
ARG
89
A
ARG
13
1
Y
1
A
ASP
90
A
ASP
14
1
Y
1
A
GLY
163
A
GLY
87
1
Y
1
A
SER
164
A
SER
88
1
Y
1
A
PRO
165
A
PRO
89
1
Y
1
A
SER
166
A
SER
90
1
Y
1
A
ARG
167
A
ARG
91
1
Y
1
A
HIS
168
A
HIS
92
1
Y
1
A
HIS
169
A
HIS
93
1
Y
1
A
HIS
170
A
HIS
94
1
Y
1
A
HIS
171
A
HIS
95
1
Y
1
A
HIS
172
A
HIS
96
1
Y
1
A
HIS
173
A
HIS
97
1
Y
1
-4.26
0.70
108.00
103.74
B
B
B
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
-4.56
0.70
108.00
103.44
B
B
B
O4'
C1'
N9
DA
DA
DA
12
12
12
N
1
-7.05
0.70
108.00
100.95
C
C
C
O4'
C1'
N9
DA
DA
DA
21
21
21
N
1
2.09
0.30
108.30
110.39
C
C
C
O4'
C1'
N1
DT
DT
DT
22
22
22
N
1
3.68
0.30
108.30
111.98
C
C
C
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
-6.90
0.70
108.00
101.10
C
C
C
O4'
C1'
N1
DT
DT
DT
30
30
30
N
1
8.06
1.20
119.70
127.76
C
C
C
C3'
O3'
P
DT
DT
DT
30
30
31
Y
1
10.11
1.20
119.70
129.81
C
C
C
C3'
O3'
P
DT
DT
DC
31
31
32
Y
1
5.03
0.30
108.30
113.33
C
C
C
O4'
C1'
N1
DC
DC
DC
32
32
32
N
1
-3.82
0.60
122.90
119.08
C
C
C
C6
C5
C7
DT
DT
DT
36
36
36
N
1
3.44
0.30
108.30
111.74
C
C
C
O4'
C1'
N9
DG
DG
DG
40
40
40
N
1
B
B
O3'
C3'
DC
DC
18
18
-0.037
0.006
1.419
1.382
N
1
A
ASN
126
-41.97
152.46
2.50
1000.00
0.250
7115
59.076
0.290
0.000
0.070
0.300
0.000
-0.490
0.955
0.924
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.276
0.212
0.215
2.500
23.480
331
7115
7115
4.700
98.530
24.894
0.266
RANDOM
1
THROUGHOUT
0.00
0.00
SAD
0.651
0.325
0.800
0.800
1.200
MAXIMUM LIKELIHOOD
MASK
2.500
23.480
47
1447
0
816
584
0.009
0.021
1512
1.848
2.628
2212
5.524
5.000
71
35.425
22.759
29
20.454
15.000
107
21.077
15.000
6
0.078
0.200
237
0.005
0.020
870
0.219
0.200
551
0.317
0.200
893
0.189
0.200
91
0.231
0.200
29
0.129
0.200
5
0.693
1.500
363
0.898
2.000
576
1.001
3.000
1553
1.579
4.500
1636
0.429
0.428
2.565
22
442
464
20
88.380
84.3
2.500
48.795
3C2I
7122
7122
0
0
0.075
0.075
1
3.100
7.100
98.500
0.377
2.50
2.64
2.0
5055
950
0.377
1
5.30
90.70
0.312
2.64
2.80
2.3
7069
1000
0.312
1
7.10
99.90
0.205
2.80
2.99
3.6
6863
921
0.205
1
7.50
100.00
0.095
2.99
3.23
2.1
6483
871
0.095
1
7.40
100.00
0.076
3.23
3.54
2.1
5886
791
0.076
1
7.40
99.90
0.069
3.54
3.95
6.2
5433
730
0.069
1
7.40
100.00
0.062
3.95
4.56
9.9
4710
636
0.062
1
7.40
100.00
0.069
4.56
5.59
8.4
4123
560
0.069
1
7.40
100.00
0.060
5.59
7.91
7.7
3118
429
0.060
1
7.30
100.00
0.056
7.91
25.66
9.6
1567
234
0.056
1
6.70
96.40
data reduction
A.G.W. Leslie
andrew@mrc-lmb.cam.ac.uk
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/
MOSFLM
package
data scaling
Phil Evans
pre@mrc-lmb.cam.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/INDEX.html
SCALA
other
phasing
Tom Terwilliger
terwilliger@LANL.gov
19-June-2006
http://www.solve.lanl.gov/
SOLVE
package
2.11
phasing
Terwilliger, T. C
terwilliger@LANL.gov
24-June-2006
http://www.solve.lanl.gov/
RESOLVE
package
2.11
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
data extraction
PDB
sw-help@rcsb.rutgers.edu
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.004
The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
SER
134
A
SER
58
HELX_P
A
GLY
146
A
GLY
70
1
1
13
covale
1.326
both
A
PRO
93
A
C
PRO
17
1_555
A
MSE
94
A
N
MSE
18
1_555
covale
1.323
both
A
MSE
94
A
C
MSE
18
1_555
A
TYR
95
A
N
TYR
19
1_555
covale
1.331
both
A
ILE
139
A
C
ILE
63
1_555
A
MSE
140
A
N
MSE
64
1_555
covale
1.329
both
A
MSE
140
A
C
MSE
64
1_555
A
TYR
141
A
N
TYR
65
1_555
covale
1.590
both
B
DA
7
B
O3'
DA
7
1_555
B
5CM
8
B
P
5CM
8
1_555
covale
1.608
both
B
5CM
8
B
O3'
5CM
8
1_555
B
DG
9
B
P
DG
9
1_555
covale
1.615
both
C
DC
32
C
O3'
DC
12
1_555
C
5CM
33
C
P
5CM
13
1_555
covale
1.597
both
C
5CM
33
C
O3'
5CM
13
1_555
C
DG
34
C
P
DG
14
1_555
hydrog
WATSON-CRICK
B
DC
2
B
N3
DC
2
1_555
C
DG
40
C
N1
DG
20
1_555
hydrog
WATSON-CRICK
B
DC
2
B
N4
DC
2
1_555
C
DG
40
C
O6
DG
20
1_555
hydrog
WATSON-CRICK
B
DC
2
B
O2
DC
2
1_555
C
DG
40
C
N2
DG
20
1_555
hydrog
WATSON-CRICK
B
DT
3
B
N3
DT
3
1_555
C
DA
39
C
N1
DA
19
1_555
hydrog
WATSON-CRICK
B
DT
3
B
O4
DT
3
1_555
C
DA
39
C
N6
DA
19
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N1
DG
4
1_555
C
DC
38
C
N3
DC
18
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N2
DG
4
1_555
C
DC
38
C
O2
DC
18
1_555
hydrog
WATSON-CRICK
B
DG
4
B
O6
DG
4
1_555
C
DC
38
C
N4
DC
18
1_555
hydrog
WATSON-CRICK
B
DG
5
B
N1
DG
5
1_555
C
DC
37
C
N3
DC
17
1_555
hydrog
WATSON-CRICK
B
DG
5
B
N2
DG
5
1_555
C
DC
37
C
O2
DC
17
1_555
hydrog
WATSON-CRICK
B
DG
5
B
O6
DG
5
1_555
C
DC
37
C
N4
DC
17
1_555
hydrog
WATSON-CRICK
B
DA
6
B
N1
DA
6
1_555
C
DT
36
C
N3
DT
16
1_555
hydrog
WATSON-CRICK
B
DA
6
B
N6
DA
6
1_555
C
DT
36
C
O4
DT
16
1_555
hydrog
WATSON-CRICK
B
DA
7
B
N1
DA
7
1_555
C
DT
35
C
N3
DT
15
1_555
hydrog
WATSON-CRICK
B
DA
7
B
N6
DA
7
1_555
C
DT
35
C
O4
DT
15
1_555
hydrog
WATSON-CRICK
B
5CM
8
B
N3
5CM
8
1_555
C
DG
34
C
N1
DG
14
1_555
hydrog
WATSON-CRICK
B
5CM
8
B
N4
5CM
8
1_555
C
DG
34
C
O6
DG
14
1_555
hydrog
WATSON-CRICK
B
5CM
8
B
O2
5CM
8
1_555
C
DG
34
C
N2
DG
14
1_555
hydrog
WATSON-CRICK
B
DG
9
B
N1
DG
9
1_555
C
5CM
33
C
N3
5CM
13
1_555
hydrog
WATSON-CRICK
B
DG
9
B
N2
DG
9
1_555
C
5CM
33
C
O2
5CM
13
1_555
hydrog
WATSON-CRICK
B
DG
9
B
O6
DG
9
1_555
C
5CM
33
C
N4
5CM
13
1_555
hydrog
WATSON-CRICK
B
DG
10
B
N1
DG
10
1_555
C
DC
32
C
N3
DC
12
1_555
hydrog
WATSON-CRICK
B
DG
10
B
N2
DG
10
1_555
C
DC
32
C
O2
DC
12
1_555
hydrog
WATSON-CRICK
B
DG
10
B
O6
DG
10
1_555
C
DC
32
C
N4
DC
12
1_555
hydrog
WATSON-CRICK
B
DA
11
B
N1
DA
11
1_555
C
DT
31
C
N3
DT
11
1_555
hydrog
WATSON-CRICK
B
DA
11
B
N6
DA
11
1_555
C
DT
31
C
O4
DT
11
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N1
DA
12
1_555
C
DT
30
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
12
B
N6
DA
12
1_555
C
DT
30
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
B
DT
13
B
N3
DT
13
1_555
C
DA
29
C
N1
DA
9
1_555
hydrog
WATSON-CRICK
B
DT
13
B
O4
DT
13
1_555
C
DA
29
C
N6
DA
9
1_555
hydrog
WATSON-CRICK
B
DT
14
B
N3
DT
14
1_555
C
DA
28
C
N1
DA
8
1_555
hydrog
WATSON-CRICK
B
DT
14
B
O4
DT
14
1_555
C
DA
28
C
N6
DA
8
1_555
hydrog
WATSON-CRICK
B
DC
15
B
N3
DC
15
1_555
C
DG
27
C
N1
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
15
B
N4
DC
15
1_555
C
DG
27
C
O6
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
15
B
O2
DC
15
1_555
C
DG
27
C
N2
DG
7
1_555
hydrog
WATSON-CRICK
B
DT
16
B
N3
DT
16
1_555
C
DA
26
C
N1
DA
6
1_555
hydrog
WATSON-CRICK
B
DT
16
B
O4
DT
16
1_555
C
DA
26
C
N6
DA
6
1_555
hydrog
WATSON-CRICK
B
DT
17
B
N3
DT
17
1_555
C
DA
25
C
N1
DA
5
1_555
hydrog
WATSON-CRICK
B
DT
17
B
O4
DT
17
1_555
C
DA
25
C
N6
DA
5
1_555
hydrog
WATSON-CRICK
B
DC
18
B
N3
DC
18
1_555
C
DG
24
C
N1
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
18
B
N4
DC
18
1_555
C
DG
24
C
O6
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
18
B
O2
DC
18
1_555
C
DG
24
C
N2
DG
4
1_555
hydrog
WATSON-CRICK
B
DT
19
B
N3
DT
19
1_555
C
DA
23
C
N1
DA
3
1_555
hydrog
WATSON-CRICK
B
DT
19
B
O4
DT
19
1_555
C
DA
23
C
N6
DA
3
1_555
hydrog
WATSON-CRICK
B
DA
20
B
N1
DA
20
1_555
C
DT
22
C
N3
DT
2
1_555
hydrog
WATSON-CRICK
B
DA
20
B
N6
DA
20
1_555
C
DT
22
C
O4
DT
2
1_555
Transcription regulator
water mediated recognition, protein-methylated DNA complex, Asx-ST-motif, Disease mutation, DNA-binding, Nucleus, Phosphoprotein, Repressor, Transcription regulator
MECP2_HUMAN
UNP
1
77
P51608
ASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFD
FTVTGRGSPSR
3C2I
PDB
2
1
3C2I
TCTGGAACGGAATTCTTCTA
3C2I
PDB
3
1
3C2I
ATAGAAGAATTCCGTTCCAG
77
167
3C2I
77
167
P51608
A
1
1
91
1
20
3C2I
1
20
3C2I
B
2
1
20
21
40
3C2I
21
40
3C2I
C
3
1
20
1
ALA
engineered mutation
MSE
140
3C2I
A
P51608
UNP
140
64
1
expression tag
HIS
168
3C2I
A
P51608
UNP
92
1
expression tag
HIS
169
3C2I
A
P51608
UNP
93
1
expression tag
HIS
170
3C2I
A
P51608
UNP
94
1
expression tag
HIS
171
3C2I
A
P51608
UNP
95
1
expression tag
HIS
172
3C2I
A
P51608
UNP
96
1
expression tag
HIS
173
3C2I
A
P51608
UNP
97
3
anti-parallel
anti-parallel
A
THR
105
A
THR
29
A
GLN
110
A
GLN
34
A
TYR
120
A
TYR
44
A
ILE
125
A
ILE
49
A
ALA
131
A
ALA
55
A
PHE
132
A
PHE
56
5
C 1 2 1