Phosphorus in PDB 195d: X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Protein crystallography data
The structure of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex, PDB code: 195d
was solved by
K.Balendiran,
S.T.Rao,
C.Y.Sekharudu,
G.Zon,
M.Sundaralingam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.490,
40.870,
67.019,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.2 /
n/a
|
Phosphorus Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
22;
Binding sites:
The binding sites of Phosphorus atom in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
(pdb code 195d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the
X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex, PDB code: 195d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 1 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:45.4
occ:1.00
|
P
|
A:DG2
|
0.0
|
45.4
|
1.0
|
OP1
|
A:DG2
|
1.5
|
44.9
|
1.0
|
OP2
|
A:DG2
|
1.5
|
44.1
|
1.0
|
O5'
|
A:DG2
|
1.6
|
43.7
|
1.0
|
O3'
|
A:DC1
|
1.7
|
42.5
|
1.0
|
C5'
|
A:DG2
|
2.7
|
39.7
|
1.0
|
C3'
|
A:DC1
|
2.7
|
38.6
|
1.0
|
C2'
|
A:DC1
|
3.6
|
37.1
|
1.0
|
C4'
|
A:DC1
|
3.9
|
37.1
|
1.0
|
C4'
|
A:DG2
|
4.0
|
36.9
|
1.0
|
O
|
A:HOH49
|
4.1
|
52.9
|
1.0
|
C3'
|
A:DG2
|
4.3
|
36.2
|
1.0
|
C1'
|
A:DC1
|
4.4
|
33.5
|
1.0
|
O
|
A:HOH82
|
4.4
|
91.2
|
1.0
|
O
|
A:HOH53
|
4.4
|
82.0
|
1.0
|
O4'
|
A:DG2
|
4.5
|
35.2
|
1.0
|
C2'
|
A:DG2
|
4.5
|
34.9
|
1.0
|
O
|
A:HOH27
|
4.7
|
42.2
|
1.0
|
O4'
|
A:DC1
|
4.8
|
35.2
|
1.0
|
C8
|
A:DG2
|
4.9
|
22.7
|
1.0
|
|
Phosphorus binding site 2 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 2 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:36.0
occ:1.00
|
P
|
A:DC3
|
0.0
|
36.0
|
1.0
|
OP1
|
A:DC3
|
1.5
|
36.2
|
1.0
|
OP2
|
A:DC3
|
1.5
|
35.6
|
1.0
|
O3'
|
A:DG2
|
1.6
|
37.8
|
1.0
|
O5'
|
A:DC3
|
1.6
|
33.0
|
1.0
|
C3'
|
A:DG2
|
2.5
|
36.2
|
1.0
|
C5'
|
A:DC3
|
2.6
|
31.7
|
1.0
|
C2'
|
A:DG2
|
3.2
|
34.9
|
1.0
|
O
|
A:HOH56
|
3.7
|
91.8
|
1.0
|
O
|
A:HOH34
|
3.8
|
35.8
|
1.0
|
C4'
|
A:DG2
|
3.8
|
36.9
|
1.0
|
C4'
|
A:DC3
|
3.8
|
29.9
|
1.0
|
O4'
|
A:DC3
|
3.9
|
28.0
|
1.0
|
C1'
|
A:DG2
|
4.2
|
31.0
|
1.0
|
O4'
|
A:DG2
|
4.5
|
35.2
|
1.0
|
C3'
|
A:DC3
|
4.5
|
28.5
|
1.0
|
O
|
A:HOH38
|
4.6
|
0.4
|
1.0
|
O
|
A:HOH82
|
4.7
|
91.2
|
1.0
|
C5'
|
A:DG2
|
4.8
|
39.7
|
1.0
|
C6
|
A:DC3
|
4.9
|
23.1
|
1.0
|
|
Phosphorus binding site 3 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 3 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:33.8
occ:1.00
|
P
|
A:DG4
|
0.0
|
33.8
|
1.0
|
OP1
|
A:DG4
|
1.5
|
39.0
|
1.0
|
OP2
|
A:DG4
|
1.5
|
32.3
|
1.0
|
O5'
|
A:DG4
|
1.6
|
34.7
|
1.0
|
O3'
|
A:DC3
|
1.6
|
30.6
|
1.0
|
C3'
|
A:DC3
|
2.6
|
28.5
|
1.0
|
C5'
|
A:DG4
|
2.7
|
32.4
|
1.0
|
C2'
|
A:DC3
|
3.3
|
27.7
|
1.0
|
O
|
A:HOH98
|
3.8
|
80.0
|
1.0
|
C4'
|
A:DC3
|
3.8
|
29.9
|
1.0
|
O
|
A:HOH104
|
4.0
|
76.4
|
1.0
|
C4'
|
A:DG4
|
4.0
|
32.3
|
1.0
|
O
|
A:HOH55
|
4.3
|
53.4
|
1.0
|
O4'
|
A:DG4
|
4.3
|
31.3
|
1.0
|
C8
|
A:DG4
|
4.4
|
20.5
|
1.0
|
C2'
|
A:DG4
|
4.5
|
28.9
|
1.0
|
C5'
|
A:DC3
|
4.5
|
31.7
|
1.0
|
C3'
|
A:DG4
|
4.6
|
31.1
|
1.0
|
C1'
|
A:DC3
|
4.7
|
27.3
|
1.0
|
O4'
|
A:DC3
|
4.9
|
28.0
|
1.0
|
C1'
|
A:DG4
|
4.9
|
27.8
|
1.0
|
O5'
|
A:DC3
|
5.0
|
33.0
|
1.0
|
|
Phosphorus binding site 4 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 4 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:34.3
occ:1.00
|
P
|
A:DT5
|
0.0
|
34.3
|
1.0
|
OP1
|
A:DT5
|
1.5
|
32.5
|
1.0
|
OP2
|
A:DT5
|
1.5
|
38.7
|
1.0
|
O5'
|
A:DT5
|
1.6
|
31.9
|
1.0
|
O3'
|
A:DG4
|
1.6
|
29.8
|
1.0
|
C5'
|
A:DT5
|
2.6
|
30.7
|
1.0
|
C3'
|
A:DG4
|
2.6
|
31.1
|
1.0
|
C2'
|
A:DG4
|
3.3
|
28.9
|
1.0
|
C4'
|
A:DT5
|
3.9
|
32.2
|
1.0
|
O
|
A:HOH68
|
3.9
|
36.8
|
1.0
|
C4'
|
A:DG4
|
3.9
|
32.3
|
1.0
|
O4'
|
A:DT5
|
4.2
|
33.1
|
1.0
|
C1'
|
A:DG4
|
4.2
|
27.8
|
1.0
|
O
|
A:HOH54
|
4.3
|
77.0
|
1.0
|
C3'
|
A:DT5
|
4.4
|
32.2
|
1.0
|
O4'
|
A:DG4
|
4.6
|
31.3
|
1.0
|
O
|
A:HOH92
|
4.8
|
0.3
|
1.0
|
C2'
|
A:DT5
|
4.8
|
32.0
|
1.0
|
|
Phosphorus binding site 5 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 5 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:35.8
occ:1.00
|
P
|
A:DT6
|
0.0
|
35.8
|
1.0
|
OP2
|
A:DT6
|
1.5
|
33.1
|
1.0
|
OP1
|
A:DT6
|
1.5
|
33.7
|
1.0
|
O3'
|
A:DT5
|
1.6
|
33.8
|
1.0
|
O5'
|
A:DT6
|
1.6
|
31.4
|
1.0
|
C3'
|
A:DT5
|
2.6
|
32.2
|
1.0
|
C5'
|
A:DT6
|
2.6
|
29.4
|
1.0
|
O
|
A:HOH50
|
3.3
|
69.2
|
1.0
|
C2'
|
A:DT5
|
3.3
|
32.0
|
1.0
|
C4'
|
A:DT5
|
3.8
|
32.2
|
1.0
|
C4'
|
A:DT6
|
3.9
|
28.7
|
1.0
|
C1'
|
A:DT5
|
4.3
|
30.1
|
1.0
|
O
|
A:HOH110
|
4.3
|
92.9
|
1.0
|
O4'
|
A:DT6
|
4.3
|
27.1
|
1.0
|
O
|
B:HOH84
|
4.4
|
42.6
|
1.0
|
C3'
|
A:DT6
|
4.6
|
29.1
|
1.0
|
O
|
A:HOH92
|
4.6
|
0.3
|
1.0
|
O4'
|
A:DT5
|
4.7
|
33.1
|
1.0
|
O
|
A:HOH68
|
4.7
|
36.8
|
1.0
|
C2'
|
A:DT6
|
4.8
|
27.9
|
1.0
|
C5'
|
A:DT5
|
4.8
|
30.7
|
1.0
|
O
|
B:HOH72
|
4.9
|
49.6
|
1.0
|
|
Phosphorus binding site 6 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 6 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:30.8
occ:1.00
|
P
|
A:DA7
|
0.0
|
30.8
|
1.0
|
OP1
|
A:DA7
|
1.5
|
32.5
|
1.0
|
OP2
|
A:DA7
|
1.5
|
30.0
|
1.0
|
O5'
|
A:DA7
|
1.6
|
28.3
|
1.0
|
O3'
|
A:DT6
|
1.6
|
29.6
|
1.0
|
C5'
|
A:DA7
|
2.6
|
28.0
|
1.0
|
C3'
|
A:DT6
|
2.7
|
29.1
|
1.0
|
C2'
|
A:DT6
|
3.6
|
27.9
|
1.0
|
C4'
|
A:DA7
|
3.9
|
28.3
|
1.0
|
C4'
|
A:DT6
|
3.9
|
28.7
|
1.0
|
O
|
A:HOH75
|
4.0
|
39.2
|
1.0
|
O4'
|
A:DA7
|
4.2
|
26.1
|
1.0
|
C3'
|
A:DA7
|
4.3
|
29.4
|
1.0
|
C1'
|
A:DT6
|
4.4
|
26.4
|
1.0
|
O4'
|
A:DT6
|
4.8
|
27.1
|
1.0
|
C2'
|
A:DA7
|
4.9
|
28.1
|
1.0
|
O
|
B:HOH97
|
4.9
|
0.5
|
1.0
|
|
Phosphorus binding site 7 out
of 22 in 195d
Go back to
Phosphorus Binding Sites List in 195d
Phosphorus binding site 7 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:33.6
occ:1.00
|
P
|
A:DA8
|
0.0
|
33.6
|
1.0
|
OP2
|
A:DA8
|
1.5
|
35.1
|
1.0
|
OP1
|
A:DA8
|
1.5
|
33.1
|
1.0
|
O3'
|
A:DA7
|
1.6
|
30.7
|
1.0
|
O5'
|
A:DA8
|
1.6
|
30.5
|
1.0
|
C5'
|
A:DA8
|
2.6
|
27.6
|
1.0
|
C3'
|
A:DA7
|
2.6
|
29.4
|
1.0
|
C2'
|
A:DA7
|
3.3
|
28.1
|
1.0
|
O
|
A:HOH91
|
3.7
|
83.1
|
1.0
|
C4'
|
A:DA8
|
3.9
|
28.1
|
1.0
|
C4'
|
A:DA7
|
3.9
|
28.3
|
1.0
|
O4'
|
A:DA8
|
4.3
|
26.4
|
1.0
|
C1'
|
A:DA7
|
4.4
|
23.8
|
1.0
|
C3'
|
A:DA8
|
4.6
|
29.1
|
1.0
|
O
|
A:HOH60
|
4.6
|
53.5
|
1.0
|
C5'
|
A:DA7
|
4.8
|
28.0
|
1.0
|
O4'
|
A:DA7
|
4.8
|
26.1
|
1.0
|
C13
|
B:NT25
|
5.0
|
37.0
|
1.0
|
|
Phosphorus binding site 8 out
of 22 in 195d
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Phosphorus Binding Sites List in 195d
Phosphorus binding site 8 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P9
b:34.1
occ:1.00
|
P
|
A:DC9
|
0.0
|
34.1
|
1.0
|
OP2
|
A:DC9
|
1.5
|
33.3
|
1.0
|
OP1
|
A:DC9
|
1.5
|
33.0
|
1.0
|
O5'
|
A:DC9
|
1.6
|
32.7
|
1.0
|
O3'
|
A:DA8
|
1.6
|
35.3
|
1.0
|
C5'
|
A:DC9
|
2.6
|
34.4
|
1.0
|
C3'
|
A:DA8
|
2.7
|
29.1
|
1.0
|
C2'
|
A:DA8
|
3.4
|
27.1
|
1.0
|
O
|
A:HOH103
|
3.9
|
67.8
|
1.0
|
C4'
|
A:DC9
|
3.9
|
36.9
|
1.0
|
C4'
|
A:DA8
|
3.9
|
28.1
|
1.0
|
O4'
|
A:DC9
|
4.2
|
36.4
|
1.0
|
O
|
A:HOH29
|
4.3
|
57.1
|
1.0
|
C1'
|
A:DA8
|
4.3
|
24.7
|
1.0
|
C3'
|
A:DC9
|
4.4
|
39.1
|
1.0
|
O
|
A:HOH112
|
4.4
|
82.0
|
1.0
|
C2'
|
A:DC9
|
4.8
|
37.0
|
1.0
|
O4'
|
A:DA8
|
4.8
|
26.4
|
1.0
|
C5'
|
A:DA8
|
4.9
|
27.6
|
1.0
|
|
Phosphorus binding site 9 out
of 22 in 195d
Go back to
Phosphorus Binding Sites List in 195d
Phosphorus binding site 9 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P10
b:47.4
occ:1.00
|
P
|
A:DG10
|
0.0
|
47.4
|
1.0
|
OP1
|
A:DG10
|
1.5
|
45.9
|
1.0
|
OP2
|
A:DG10
|
1.5
|
43.9
|
1.0
|
O3'
|
A:DC9
|
1.6
|
43.1
|
1.0
|
O5'
|
A:DG10
|
1.6
|
46.3
|
1.0
|
C3'
|
A:DC9
|
2.5
|
39.1
|
1.0
|
C5'
|
A:DG10
|
2.7
|
44.4
|
1.0
|
C2'
|
A:DC9
|
3.5
|
37.0
|
1.0
|
C4'
|
A:DC9
|
3.8
|
36.9
|
1.0
|
O
|
A:HOH29
|
3.9
|
57.1
|
1.0
|
C4'
|
A:DG10
|
3.9
|
43.7
|
1.0
|
O4'
|
A:DG10
|
4.2
|
41.5
|
1.0
|
C1'
|
A:DC9
|
4.5
|
34.9
|
1.0
|
C3'
|
A:DG10
|
4.5
|
44.5
|
1.0
|
C5'
|
A:DC9
|
4.6
|
34.4
|
1.0
|
C2'
|
A:DG10
|
4.6
|
41.2
|
1.0
|
O
|
A:HOH112
|
4.7
|
82.0
|
1.0
|
O4'
|
A:DC9
|
4.8
|
36.4
|
1.0
|
C1'
|
A:DG10
|
5.0
|
37.5
|
1.0
|
|
Phosphorus binding site 10 out
of 22 in 195d
Go back to
Phosphorus Binding Sites List in 195d
Phosphorus binding site 10 out
of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P11
b:53.0
occ:1.00
|
P
|
A:DC11
|
0.0
|
53.0
|
1.0
|
OP2
|
A:DC11
|
1.5
|
53.8
|
1.0
|
OP1
|
A:DC11
|
1.5
|
55.4
|
1.0
|
O5'
|
A:DC11
|
1.6
|
52.8
|
1.0
|
O3'
|
A:DG10
|
1.6
|
47.5
|
1.0
|
C3'
|
A:DG10
|
2.7
|
44.5
|
1.0
|
C5'
|
A:DC11
|
2.7
|
49.4
|
1.0
|
C4'
|
A:DG10
|
3.7
|
43.7
|
1.0
|
C2'
|
A:DG10
|
3.8
|
41.2
|
1.0
|
O
|
A:HOH100
|
3.8
|
79.3
|
1.0
|
C4'
|
A:DC11
|
3.8
|
47.8
|
1.0
|
O4'
|
A:DC11
|
3.9
|
46.3
|
1.0
|
C6
|
A:DC11
|
4.2
|
38.6
|
1.0
|
C2'
|
A:DC11
|
4.5
|
45.1
|
1.0
|
C3'
|
A:DC11
|
4.5
|
47.5
|
1.0
|
C1'
|
A:DG10
|
4.5
|
37.5
|
1.0
|
O
|
A:HOH26
|
4.7
|
66.1
|
1.0
|
C5'
|
A:DG10
|
4.7
|
44.4
|
1.0
|
C1'
|
A:DC11
|
4.7
|
42.6
|
1.0
|
O4'
|
A:DG10
|
4.8
|
41.5
|
1.0
|
C5
|
A:DC11
|
4.9
|
36.9
|
1.0
|
N1
|
A:DC11
|
5.0
|
38.8
|
1.0
|
|
Reference:
K.Balendiran,
S.T.Rao,
C.Y.Sekharudu,
G.Zon,
M.Sundaralingam.
X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex. Acta Crystallogr.,Sect.D V. 51 190 1995.
ISSN: ISSN 0907-4449
PubMed: 15299320
DOI: 10.1107/S0907444994010759
Page generated: Fri Sep 25 11:51:53 2020
|