0.055935
0.000000
0.000000
0.000000
0.032289
0.000000
0.000000
0.000000
0.023039
0.00000
0.00000
0.00000
Venkadesh, S.
Mandal, P.K.
Kannan, R.
Gautham, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
17.878
30.970
43.405
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
non-polymer
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
H2 O
18.015
WATER
non-polymer
Mn 2
54.938
MANGANESE (II) ION
non-polymer
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
N
C
N
12
R
C
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
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
N
N
36
N
C
N
37
N
N
N
38
N
C
N
39
N
C
N
40
N
C
N
41
N
O
N
42
N
N
N
43
R
C
N
44
N
C
N
45
S
C
N
46
R
C
N
47
N
O
N
48
N
O
N
49
N
C
N
50
N
O
N
51
N
P
N
52
N
O
N
53
N
O
N
54
N
O
N
55
N
H
N
56
N
H
N
57
N
H
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
O
N
70
N
P
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
C
N
75
R
C
N
76
N
O
N
77
S
C
N
78
N
O
N
79
N
C
N
80
R
C
Y
81
N
N
Y
82
N
C
Y
83
N
N
Y
84
N
C
N
85
N
C
N
86
N
O
N
87
N
N
N
88
N
C
N
89
N
N
N
90
N
N
Y
91
N
C
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
O
N
107
N
P
N
108
N
O
N
109
N
O
N
110
N
O
N
111
N
C
N
112
R
C
N
113
N
O
N
114
S
C
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
N
N
119
N
C
N
120
N
O
N
121
N
N
N
122
N
C
N
123
N
O
N
124
N
C
N
125
N
C
N
126
N
C
N
127
N
H
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
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
O
N
143
N
H
N
144
N
H
N
145
N
MN
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
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
doub
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
doub
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
doub
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
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
doub
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
Y
94
N
sing
Y
95
N
sing
Y
96
N
doub
N
97
N
sing
Y
98
N
sing
N
99
N
sing
Y
100
N
doub
N
101
N
doub
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
doub
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
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
doub
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
To be Published
0353
Crystal studies of d(CACGCG).d(CGCGTG) grown with various counter ions
10.2210/pdb3g2r/pdb
pdb_00003g2r
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
mirrors
IMAGE PLATE
2008-11-20
MARRESEARCH
mirror
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
BRUKER AXS MICROSTAR
1825.216
5'-D(*CP*GP*TP*GP*CP*G)-3'
1
syn
polymer
307.197
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
1
syn
non-polymer
54.938
MANGANESE (II) ION
1
syn
non-polymer
18.015
water
6
nat
water
no
no
(DC)(DG)(DT)(DG)(DC)(DG)
CGTGCG
A
polydeoxyribonucleotide
n
n
n
n
n
n
1
VAPOR DIFFUSION, HANGING DROP
6.99
50mM Sodium cacodylate, 5mM MnCl2, 1mM Spermine, 50% methyl pentane diol, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
Sodium cacoldylate
1
MnCl2
1
Spermine
1
MPD
1
Sodium cacoldylate
2
MnCl2
2
MPD
2
-7.096
1
19
A
1
A
4
-1.170
A_DC1:DG4_A
1
6.716
-1.227
-0.037
-0.099
11.528
A
2
A
3
4.713
A_DG2:DT3_A
2
-5.397
0.396
0.857
-0.051
-11.528
A
3
A
2
4.713
A_DT3:DG2_A
3
-5.397
-0.396
0.857
-0.051
7.096
1
19
A
4
A
1
-1.170
A_DG4:DC1_A
4
6.716
1.227
-0.037
-0.099
0.208
-9.167
A
A
1
2
-23.696
A
A
4
3
3.333
3.270
0.040
5.122
AA_DC1DG2:DT3DG4_AA
1
-6.557
-47.514
-5.512
-36.978
-9.637
4.502
-48.812
A
A
2
3
-6.507
A
A
3
2
4.351
5.368
0.000
-1.688
AA_DG2DT3:DG2DT3_AA
2
0.000
0.000
-48.534
1.488
0.000
0.208
-9.167
A
A
3
4
-23.696
A
A
2
1
3.333
3.270
-0.040
5.122
AA_DT3DG4:DC1DG2_AA
3
6.557
47.514
-5.512
-36.978
9.637
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2009-03-03
1
1
2011-07-13
1
2
2024-03-20
_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
Crystal structure of d(CACGCG)d(CGCGTG) grown in presence of MnCl2
RCSB
Y
PDBJ
2009-02-01
REL
REL
DCM
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
MN
MANGANESE (II) ION
HOH
water
C
7
2
DCM
DCM
7
A
MN
1
3
MN
MN
8
A
HOH
1
4
HOH
HOH
9
A
HOH
2
4
HOH
HOH
10
A
HOH
3
4
HOH
HOH
11
A
HOH
4
4
HOH
HOH
12
A
HOH
5
4
HOH
HOH
13
A
HOH
7
4
HOH
HOH
14
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
software_defined_assembly
PISA
2
dimeric
480
-9
2520
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_565
x,-y+1,-z
crystal symmetry operation
0.0000000000
30.9700000000
0.0000000000
1
A
MN
8
C
MN
1
A
N1
DCM
7
B
N1
DCM
1
1
N
1
A
C2
DCM
7
B
C2
DCM
1
1
N
1
A
N3
DCM
7
B
N3
DCM
1
1
N
1
A
C4
DCM
7
B
C4
DCM
1
1
N
1
A
C5
DCM
7
B
C5
DCM
1
1
N
1
A
C6
DCM
7
B
C6
DCM
1
1
N
1
A
O2
DCM
7
B
O2
DCM
1
1
N
1
A
N4
DCM
7
B
N4
DCM
1
1
N
1
A
C1'
DCM
7
B
C1'
DCM
1
1
N
1
A
C2'
DCM
7
B
C2'
DCM
1
1
N
1
A
C3'
DCM
7
B
C3'
DCM
1
1
N
1
A
C4'
DCM
7
B
C4'
DCM
1
1
N
1
A
O4'
DCM
7
B
O4'
DCM
1
1
N
1
A
O3'
DCM
7
B
O3'
DCM
1
1
N
1
A
C5'
DCM
7
B
C5'
DCM
1
1
N
1
A
O5'
DCM
7
B
O5'
DCM
1
1
N
1
A
O3P
DCM
7
B
O3P
DCM
1
1
N
1
A
A
O3'
P
DG
DCM
6
7
1.89
1
-5.55
0.80
102.40
96.85
A
A
A
C3'
C2'
C1'
DC
DC
DC
1
1
1
N
1
-10.24
0.70
108.00
97.76
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-18.67
1.60
120.90
102.23
A
A
A
P
O5'
C5'
DG
DG
DG
2
2
2
N
1
4.89
0.60
106.00
110.89
A
A
A
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
-9.71
0.70
108.00
98.29
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.75
0.50
111.90
115.65
A
A
A
C2
N3
C4
DG
DG
DG
2
2
2
N
1
-3.30
0.50
128.60
125.30
A
A
A
N3
C4
C5
DG
DG
DG
2
2
2
N
1
-4.24
0.40
110.80
106.56
A
A
A
C4
C5
N7
DG
DG
DG
2
2
2
N
1
3.72
0.50
104.30
108.02
A
A
A
C5
N7
C8
DG
DG
DG
2
2
2
N
1
3.97
0.60
130.40
134.37
A
A
A
C6
C5
N7
DG
DG
DG
2
2
2
N
1
-6.18
0.60
119.90
113.72
A
A
A
N1
C6
O6
DG
DG
DG
2
2
2
N
1
4.88
0.60
128.60
133.48
A
A
A
C5
C6
O6
DG
DG
DG
2
2
2
N
1
3.35
0.30
108.30
111.65
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
-5.15
0.40
104.50
99.35
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
8.14
1.20
119.70
127.84
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
1
-3.24
0.40
104.50
101.26
A
A
A
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
1
8.57
1.40
114.30
122.87
A
A
A
N1
C1'
C2'
DC
DC
DC
5
5
5
N
1
-14.13
0.70
108.00
93.87
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
3.47
0.50
119.90
123.37
A
A
A
C2
N3
C4
DC
DC
DC
5
5
5
N
1
6.47
0.60
118.90
125.37
A
A
A
N1
C2
O2
DC
DC
DC
5
5
5
N
1
-12.73
1.90
104.00
91.27
A
A
A
O3'
P
O5'
DC
DG
DG
5
6
6
Y
1
9.04
1.20
110.70
119.74
A
A
A
O5'
P
OP1
DG
DG
DG
6
6
6
N
1
-11.82
1.60
120.90
109.08
A
A
A
P
O5'
C5'
DG
DG
DG
6
6
6
N
1
-5.39
0.40
104.50
99.11
A
A
A
O4'
C4'
C3'
DG
DG
DG
6
6
6
N
1
-3.50
0.50
128.60
125.10
A
A
A
N3
C4
C5
DG
DG
DG
6
6
6
N
1
-3.36
0.50
111.50
108.14
A
A
A
C5
C6
N1
DG
DG
DG
6
6
6
N
1
-4.65
0.40
110.80
106.15
A
A
A
C4
C5
N7
DG
DG
DG
6
6
6
N
1
3.88
0.50
104.30
108.18
A
A
A
C5
N7
C8
DG
DG
DG
6
6
6
N
1
2.45
0.40
105.40
107.85
A
A
A
N9
C4
C5
DG
DG
DG
6
6
6
N
1
6.07
0.60
128.60
134.67
A
A
A
C5
C6
O6
DG
DG
DG
6
6
6
N
1
A
A
C6
O6
DG
DG
6
6
0.063
0.009
1.237
1.300
N
30.334
-1.12
0.00
0.00
-0.45
0.00
1.57
0.934
0.950
0.27015
0.26859
0.26870
2.15
14.70
41
694
693
5.6
99.73
7.295
0.188
RANDOM
1
isotropic
THROUGHOUT
MOLECULAR REPLACEMENT
0.390
0.258
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
2.15
14.70
6
131
4
121
0
0.021
0.021
138
4.056
3.000
211
0.128
0.200
23
0.017
0.020
64
0.227
0.200
53
0.345
0.200
74
0.451
0.200
3
0.459
0.200
22
0.688
0.200
3
0.066
0.358
2.208
1
55
55
20
100.00
40.616
2.15
15
3G2R
751
742
0.0410
0.0383
1
8.0
3.83
98.8
0.2377
2.15
2.23
2.0
82
0.2162
3.87
100
data collection
MAR345dtb
phasing
AMoRE
refinement
REFMAC
5.2.0019
data reduction
AUTOMAR
data scaling
SCALEPACK
N
Crystal structure of d(CACGCG).d(CGCGTG) cocrystallized with MnCl2
1
N
N
2
N
N
3
N
N
4
N
N
The author states that there is no possible quaternary structure
metalc
2.439
A
DG
2
A
O6
DG
2
1_555
A
MN
8
C
MN
MN
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
4
A
N1
DG
4
4_565
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
4
A
O6
DG
4
4_565
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
4
A
N2
DG
4
4_565
hydrog
DG-DT MISPAIR
A
DG
2
A
N2
DG
2
1_555
A
DT
3
A
O2
DT
3
4_565
hydrog
DT-DG MISPAIR
A
DT
3
A
N3
DT
3
1_555
A
DG
2
A
O6
DG
2
4_565
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
1
A
N3
DC
1
4_565
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
1
A
O2
DC
1
4_565
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
1
A
N4
DC
1
4_565
DNA
duplex Z-form DNA with Watson-Crick base pairing, DNA
3G2R
PDB
1
3G2R
1
6
3G2R
1
6
3G2R
A
1
1
6
BINDING SITE FOR RESIDUE DCM A 7
A
DCM
7
Software
3
BINDING SITE FOR RESIDUE MN A 8
A
MN
8
Software
3
A
DC
1
A
DC
1
3
2_565
A
DG
4
A
DG
4
3
7_455
A
DG
6
A
DG
6
3
1_555
A
DG
2
A
DG
2
3
1_555
A
DT
3
A
DT
3
3
1_555
A
HOH
10
D
HOH
3
1_555
20
C 2 2 21