0.055975
0.000000
0.000000
0.000000
0.032444
0.000000
0.000000
0.000000
0.022323
0.00000
0.00000
0.00000
Schroth, G.P.
Kagawa, T.F.
Shing Ho, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
17.865
30.822
44.797
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
C10 H15 N3 O4
241.244
n
5-METHYL-2'-DEOXYCYTIDINE
DNA linking
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
C
N
57
N
C
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
Y
84
N
N
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
N
Y
94
N
C
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
O
N
110
N
H
N
111
N
H
N
112
N
N
N
113
N
C
N
114
N
N
N
115
N
C
N
116
N
C
N
117
N
C
N
118
N
O
N
119
N
N
N
120
R
C
N
121
N
C
N
122
S
C
N
123
R
C
N
124
N
O
N
125
N
O
N
126
N
C
N
127
N
O
N
128
N
C
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
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
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
doub
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
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
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
doub
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
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
doub
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
doub
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
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
US
Biochemistry
BICHAW
0033
0006-2960
32
13381
13392
10.1021/bi00212a002
8257675
Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG).
1993
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
10
7879
7892
Molecular Structure of (m5dC-dG)3: The Role of the Methyl Group on 5-Methyl Cytosine in Stabilizing Z-DNA
1982
10.2210/pdb145d/pdb
pdb_0000145d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ROOM TEMPERATURE
1
DIFFRACTOMETER
SIEMENS
SINGLE WAVELENGTH
M
x-ray
1
1.0
ROTATING ANODE
SIEMENS
1798.303
DNA (5'-D(*(MCY)P*GP*GP*GP*(5CM)P*G)-3')
1
syn
polymer
1718.255
DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3')
2
syn
polymer
1878.283
DNA (5'-D(*(5CM)P*DGP*DGP*DGP*(5CM)P*DG)-3')
1
syn
polymer
18.015
water
48
nat
water
no
yes
(MCY)(DG)(DG)(DG)(5CM)(DG)
CGGGCG
A
polydeoxyribonucleotide
no
yes
(MCY)(DG)(DC)(DC)(5CM)(DG)
CGCCCG
B,C
polydeoxyribonucleotide
no
yes
(5CM)(DG)(DG)(DG)(5CM)(DG)
CGGGCG
D
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
VAPOR DIFFUSION
7.00
pH 7.00, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
MGCL2
1
SPERMIDINE
1
WATER
2
MPD
2
3.039
1
19
A
1
B
12
-1.153
A_MCY1:DG12_B
1
0.768
-0.403
0.007
-0.109
-2.423
1
19
A
2
B
11
2.615
A_DG2:5CM11_B
2
0.384
0.431
0.112
-0.291
13.709
1
19
A
3
B
10
3.019
A_DG3:DC10_B
3
0.078
0.033
0.617
-0.119
-6.824
1
19
A
4
B
9
3.078
A_DG4:DC9_B
4
0.879
0.378
-0.014
-0.154
4.290
1
19
A
5
B
8
1.472
A_5CM5:DG8_B
5
-3.670
-0.302
-0.015
-0.100
-3.420
1
19
A
6
B
7
2.757
A_DG6:MCY7_B
6
-3.102
0.190
-0.096
-0.124
3.819
-10.042
A
A
1
2
1.192
B
B
12
11
3.703
-0.208
0.190
5.575
AA_MCY1DG2:5CM11DG12_BB
1
-0.992
-5.676
-9.990
-31.407
-1.039
3.126
-49.786
A
A
2
3
-1.043
B
B
11
10
3.106
0.878
0.210
-0.906
AA_DG2DG3:DC105CM11_BB
2
-2.247
-2.670
-49.732
1.015
0.093
5.116
-11.547
A
A
3
4
12.069
B
B
10
9
4.272
-2.366
-0.004
5.727
AA_DG3DG4:DC9DC10_BB
3
3.763
19.195
-10.660
-23.507
7.863
3.368
-50.458
A
A
4
5
-0.201
B
B
9
8
3.360
0.171
-0.358
-1.026
AA_DG45CM5:DG8DC9_BB
4
0.772
0.905
-50.452
1.191
-0.364
5.422
-11.659
A
A
5
6
21.952
B
B
8
7
3.675
-4.344
0.096
5.494
AA_5CM5DG6:MCY7DG8_BB
5
1.191
6.017
-10.756
-18.395
2.843
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1994-01-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_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_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_comp_id
_struct_conn.ptnr2_label_seq_id
BNL
Y
NDB
1993-11-11
REL
REL
HOH
water
HOH
31
4
HOH
HOH
31
A
HOH
37
4
HOH
HOH
37
A
HOH
41
4
HOH
HOH
41
A
HOH
44
4
HOH
HOH
44
A
HOH
53
4
HOH
HOH
53
A
HOH
58
4
HOH
HOH
58
A
HOH
67
4
HOH
HOH
67
A
HOH
70
4
HOH
HOH
70
A
HOH
71
4
HOH
HOH
71
A
HOH
72
4
HOH
HOH
72
A
HOH
25
4
HOH
HOH
25
B
HOH
34
4
HOH
HOH
34
B
HOH
38
4
HOH
HOH
38
B
HOH
40
4
HOH
HOH
40
B
HOH
42
4
HOH
HOH
42
B
HOH
45
4
HOH
HOH
45
B
HOH
46
4
HOH
HOH
46
B
HOH
47
4
HOH
HOH
47
B
HOH
50
4
HOH
HOH
50
B
HOH
52
4
HOH
HOH
52
B
HOH
55
4
HOH
HOH
55
B
HOH
26
4
HOH
HOH
26
C
HOH
27
4
HOH
HOH
27
C
HOH
29
4
HOH
HOH
29
C
HOH
32
4
HOH
HOH
32
C
HOH
35
4
HOH
HOH
35
C
HOH
39
4
HOH
HOH
39
C
HOH
43
4
HOH
HOH
43
C
HOH
48
4
HOH
HOH
48
C
HOH
51
4
HOH
HOH
51
C
HOH
54
4
HOH
HOH
54
C
HOH
60
4
HOH
HOH
60
C
HOH
61
4
HOH
HOH
61
C
HOH
62
4
HOH
HOH
62
C
HOH
64
4
HOH
HOH
64
C
HOH
66
4
HOH
HOH
66
C
HOH
28
4
HOH
HOH
28
D
HOH
30
4
HOH
HOH
30
D
HOH
33
4
HOH
HOH
33
D
HOH
36
4
HOH
HOH
36
D
HOH
49
4
HOH
HOH
49
D
HOH
56
4
HOH
HOH
56
D
HOH
57
4
HOH
HOH
57
D
HOH
59
4
HOH
HOH
59
D
HOH
63
4
HOH
HOH
63
D
HOH
65
4
HOH
HOH
65
D
HOH
68
4
HOH
HOH
68
D
HOH
69
4
HOH
HOH
69
D
MCY
1
n
1
MCY
1
A
DG
2
n
2
DG
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
5CM
5
n
5
5CM
5
A
DG
6
n
6
DG
6
A
MCY
7
n
1
MCY
7
B
DG
8
n
2
DG
8
B
DC
9
n
3
DC
9
B
DC
10
n
4
DC
10
B
5CM
11
n
5
5CM
11
B
DG
12
n
6
DG
12
B
MCY
13
n
1
MCY
13
C
DG
14
n
2
DG
14
C
DC
15
n
3
DC
15
C
DC
16
n
4
DC
16
C
5CM
17
n
5
5CM
17
C
DG
18
n
6
DG
18
C
MCY
19
n
1
5CM
19
D
DG
20
n
2
DG
20
D
DG
21
n
3
DG
21
D
DG
22
n
4
DG
22
D
5CM
23
n
5
5CM
23
D
DG
24
n
6
DG
24
D
author_defined_assembly
2
dimeric
author_defined_assembly
2
dimeric
A
MCY
1
5-METHYL-2'-DEOXYCYTIDINE
A
MCY
1
DC
A
5CM
5
A
5CM
5
DC
B
MCY
7
5-METHYL-2'-DEOXYCYTIDINE
B
MCY
1
DC
B
5CM
11
B
5CM
5
DC
C
MCY
13
5-METHYL-2'-DEOXYCYTIDINE
C
MCY
1
DC
C
5CM
17
C
5CM
5
DC
D
5CM
19
D
5CM
1
DC
D
5CM
23
D
5CM
5
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
1
B
B
O
H2
HOH
HOH
25
46
1.44
1
D
D
H2
O
HOH
HOH
56
57
1.45
1
A
C
H2
O
HOH
HOH
53
54
1.56
1
A
DG
2
A
0.063
SIDE CHAIN
1
3.04
0.50
113.10
116.14
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
A
A
A
N
1
8.08
1.20
119.70
127.78
A
A
A
C3'
O3'
P
DG
DG
DG
2
2
3
A
A
A
Y
1
-5.59
0.70
108.00
102.41
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
A
A
A
N
1
3.79
0.60
106.00
109.79
A
A
A
O4'
C4'
C3'
DG
DG
DG
6
6
6
A
A
A
N
1
-4.71
0.70
102.20
97.49
A
A
A
C4'
C3'
C2'
DG
DG
DG
6
6
6
A
A
A
N
1
3.55
0.50
113.10
116.65
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
A
A
A
N
1
3.45
0.50
106.80
110.25
B
B
B
O4'
C1'
C2'
DG
DG
DG
8
8
8
A
A
A
N
1
8.65
1.20
119.70
128.35
B
B
B
C3'
O3'
P
5CM
5CM
DG
11
11
12
A
A
A
Y
1
3.50
0.50
113.10
116.60
C
C
C
N7
C8
N9
DG
DG
DG
14
14
14
B
B
B
N
1
2.38
0.30
108.30
110.68
C
C
C
O4'
C1'
N1
DC
DC
DC
15
15
15
B
B
B
N
1
3.53
0.30
108.30
111.83
C
C
C
O4'
C1'
N1
DC
DC
DC
16
16
16
B
B
B
N
1
8.60
1.20
119.70
128.30
D
D
D
C3'
O3'
P
5CM
5CM
DG
19
19
20
B
B
B
Y
1
2.41
0.30
108.30
110.71
D
D
D
O4'
C1'
N9
DG
DG
DG
20
20
20
B
B
B
N
1
3.00
0.50
113.10
116.10
D
D
D
N7
C8
N9
DG
DG
DG
20
20
20
B
B
B
N
1
3.27
0.50
113.10
116.37
D
D
D
N7
C8
N9
DG
DG
DG
21
21
21
B
B
B
N
1
3.47
0.50
113.10
116.57
D
D
D
N7
C8
N9
DG
DG
DG
22
22
22
B
B
B
N
1
A
A
C8
N9
DG
DG
4
4
-0.046
0.007
1.374
1.328
A
A
N
0.193
1.250
8.000
5029
1
1.500
1.250
8.000
144
920
0
776
0
refinement
NUCLSQ
Structure and thermodynamics of nonalternating C/G base pairs in Z-DNA: the 1.3 angstroms crystal structure of the asymmetric hexanucleotide D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG)
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
covale
1.601
both
A
A
A
MCY
1
A
O3'
MCY
1
1_555
A
DG
2
A
P
DG
2
1_555
covale
1.619
both
A
A
A
DG
4
A
O3'
DG
4
1_555
A
5CM
5
A
P
5CM
5
1_555
covale
1.610
both
A
A
A
5CM
5
A
O3'
5CM
5
1_555
A
DG
6
A
P
DG
6
1_555
covale
1.579
both
A
A
B
MCY
7
B
O3'
MCY
1
1_555
B
DG
8
B
P
DG
2
1_555
covale
1.619
both
A
A
B
DC
10
B
O3'
DC
4
1_555
B
5CM
11
B
P
5CM
5
1_555
covale
1.609
both
A
A
B
5CM
11
B
O3'
5CM
5
1_555
B
DG
12
B
P
DG
6
1_555
covale
1.611
both
B
B
C
MCY
13
C
O3'
MCY
1
1_555
C
DG
14
C
P
DG
2
1_555
covale
1.641
both
B
B
C
DC
16
C
O3'
DC
4
1_555
C
5CM
17
C
P
5CM
5
1_555
covale
1.585
both
B
B
C
5CM
17
C
O3'
5CM
5
1_555
C
DG
18
C
P
DG
6
1_555
covale
1.622
both
B
B
D
5CM
19
D
O3'
5CM
1
1_555
D
DG
20
D
P
DG
2
1_555
covale
1.603
both
B
B
D
DG
22
D
O3'
DG
4
1_555
D
5CM
23
D
P
5CM
5
1_555
covale
1.615
both
B
B
D
5CM
23
D
O3'
5CM
5
1_555
D
DG
24
D
P
DG
6
1_555
hydrog
WATSON-CRICK
A
A
A
MCY
1
A
N3
MCY
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
A
A
MCY
1
A
N4
MCY
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
A
A
MCY
1
A
O2
MCY
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
A
A
DG
2
A
N1
DG
2
1_555
B
5CM
11
B
N3
5CM
5
1_555
hydrog
WATSON-CRICK
A
A
A
DG
2
A
N2
DG
2
1_555
B
5CM
11
B
O2
5CM
5
1_555
hydrog
WATSON-CRICK
A
A
A
DG
2
A
O6
DG
2
1_555
B
5CM
11
B
N4
5CM
5
1_555
hydrog
WATSON-CRICK
A
A
A
DG
3
A
N1
DG
3
1_555
B
DC
10
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
A
A
DG
3
A
N2
DG
3
1_555
B
DC
10
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
A
A
DG
3
A
O6
DG
3
1_555
B
DC
10
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
A
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
A
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
A
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
A
A
5CM
5
A
N3
5CM
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
A
A
5CM
5
A
N4
5CM
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
A
A
5CM
5
A
O2
5CM
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
A
A
DG
6
A
N1
DG
6
1_555
B
MCY
7
B
N3
MCY
1
1_555
hydrog
WATSON-CRICK
A
A
A
DG
6
A
N2
DG
6
1_555
B
MCY
7
B
O2
MCY
1
1_555
hydrog
WATSON-CRICK
A
A
A
DG
6
A
O6
DG
6
1_555
B
MCY
7
B
N4
MCY
1
1_555
DNA
Z-DNA, DOUBLE HELIX, MODIFIED, DNA
145D
PDB
1
145D
145D
PDB
2
145D
145D
PDB
3
145D
1
6
145D
1
6
145D
A
1
1
6
7
12
145D
7
12
145D
B
2
1
6
13
18
145D
13
18
145D
C
2
1
6
19
24
145D
19
24
145D
D
3
1
6
19
P 21 21 21