Ruthenium in PDB 5ls8: Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Protein crystallography data
The structure of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex, PDB code: 5ls8
was solved by
K.T.Mcquaid,
H.Abell,
J.P.Hall,
C.J.Cardin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.72 /
1.78
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.625,
36.625,
136.104,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.4 /
23.3
|
Other elements in 5ls8:
The structure of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex also contains other interesting chemical elements:
Ruthenium Binding Sites:
The binding sites of Ruthenium atom in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
(pdb code 5ls8). This binding sites where shown within
5.0 Angstroms radius around Ruthenium atom.
In total 6 binding sites of Ruthenium where determined in the
Light-Activated Ruthenium Complex Bound to A Dna Quadruplex, PDB code: 5ls8:
Jump to Ruthenium binding site number:
1;
2;
3;
4;
5;
6;
Ruthenium binding site 1 out
of 6 in 5ls8
Go back to
Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 1 out
of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 1 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru101
b:38.0
occ:1.00
|
RU
|
A:QHL101
|
0.0
|
38.0
|
1.0
|
N1
|
A:QHL101
|
1.8
|
37.0
|
1.0
|
N9
|
A:QHL101
|
1.8
|
40.0
|
1.0
|
N12
|
A:QHL101
|
1.8
|
42.6
|
1.0
|
N8
|
A:QHL101
|
1.8
|
49.5
|
1.0
|
N5
|
A:QHL101
|
1.8
|
50.1
|
1.0
|
N2
|
A:QHL101
|
1.8
|
39.0
|
1.0
|
C29
|
A:QHL101
|
2.7
|
39.7
|
1.0
|
C10
|
A:QHL101
|
2.7
|
33.2
|
1.0
|
C36
|
A:QHL101
|
2.7
|
39.6
|
1.0
|
C26
|
A:QHL101
|
2.7
|
46.7
|
1.0
|
C19
|
A:QHL101
|
2.7
|
48.8
|
1.0
|
C1
|
A:QHL101
|
2.7
|
35.0
|
1.0
|
C12
|
A:QHL101
|
2.8
|
44.7
|
1.0
|
C30
|
A:QHL101
|
2.9
|
42.3
|
1.0
|
C38
|
A:QHL101
|
2.9
|
45.5
|
1.0
|
C28
|
A:QHL101
|
2.9
|
48.6
|
1.0
|
C2
|
A:QHL101
|
2.9
|
33.7
|
1.0
|
C20
|
A:QHL101
|
2.9
|
41.0
|
1.0
|
C32
|
A:QHL101
|
4.0
|
40.3
|
1.0
|
C35
|
A:QHL101
|
4.0
|
43.2
|
1.0
|
C25
|
A:QHL101
|
4.1
|
54.7
|
1.0
|
C8
|
A:QHL101
|
4.1
|
33.2
|
1.0
|
C22
|
A:QHL101
|
4.1
|
53.5
|
1.0
|
C5
|
A:QHL101
|
4.1
|
22.7
|
1.0
|
C11
|
A:QHL101
|
4.1
|
40.3
|
1.0
|
C31
|
A:QHL101
|
4.1
|
40.0
|
1.0
|
C37
|
A:QHL101
|
4.1
|
43.8
|
1.0
|
C27
|
A:QHL101
|
4.1
|
48.5
|
1.0
|
C21
|
A:QHL101
|
4.2
|
50.8
|
1.0
|
C3
|
A:QHL101
|
4.2
|
33.5
|
1.0
|
N10
|
A:QHL101
|
4.6
|
41.3
|
1.0
|
C9
|
A:QHL101
|
4.6
|
41.9
|
1.0
|
N7
|
A:QHL101
|
4.6
|
51.8
|
1.0
|
N11
|
A:QHL101
|
4.6
|
44.0
|
1.0
|
N6
|
A:QHL101
|
4.6
|
53.3
|
1.0
|
O
|
A:HOH205
|
4.6
|
39.4
|
0.5
|
C4
|
A:QHL101
|
4.7
|
28.9
|
1.0
|
O4'
|
C:DG3
|
4.9
|
41.1
|
1.0
|
O
|
A:HOH209
|
4.9
|
50.4
|
1.0
|
|
Ruthenium binding site 2 out
of 6 in 5ls8
Go back to
Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 2 out
of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 2 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru102
b:37.6
occ:1.00
|
RU
|
A:QHL102
|
0.0
|
37.6
|
1.0
|
N12
|
A:QHL102
|
2.0
|
36.3
|
1.0
|
N8
|
A:QHL102
|
2.0
|
36.7
|
1.0
|
N9
|
A:QHL102
|
2.1
|
33.5
|
1.0
|
N5
|
A:QHL102
|
2.1
|
38.3
|
1.0
|
N2
|
A:QHL102
|
2.1
|
27.6
|
1.0
|
N1
|
A:QHL102
|
2.1
|
39.3
|
1.0
|
C36
|
A:QHL102
|
2.9
|
35.7
|
1.0
|
C29
|
A:QHL102
|
2.9
|
36.0
|
1.0
|
C26
|
A:QHL102
|
2.9
|
53.0
|
1.0
|
C19
|
A:QHL102
|
2.9
|
47.7
|
1.0
|
C1
|
A:QHL102
|
2.9
|
35.9
|
1.0
|
C10
|
A:QHL102
|
2.9
|
31.3
|
1.0
|
C38
|
A:QHL102
|
3.0
|
41.0
|
1.0
|
C28
|
A:QHL102
|
3.0
|
55.0
|
1.0
|
C2
|
A:QHL102
|
3.0
|
32.1
|
1.0
|
C30
|
A:QHL102
|
3.1
|
35.1
|
1.0
|
C12
|
A:QHL102
|
3.1
|
40.5
|
1.0
|
C20
|
A:QHL102
|
3.1
|
44.9
|
1.0
|
C35
|
A:QHL102
|
4.2
|
31.3
|
1.0
|
C32
|
A:QHL102
|
4.2
|
34.0
|
1.0
|
C25
|
A:QHL102
|
4.2
|
54.5
|
1.0
|
C5
|
A:QHL102
|
4.2
|
29.3
|
1.0
|
C22
|
A:QHL102
|
4.2
|
48.7
|
1.0
|
C8
|
A:QHL102
|
4.2
|
31.5
|
1.0
|
C37
|
A:QHL102
|
4.3
|
36.5
|
1.0
|
C27
|
A:QHL102
|
4.3
|
61.1
|
1.0
|
C3
|
A:QHL102
|
4.3
|
34.5
|
1.0
|
C31
|
A:QHL102
|
4.3
|
38.9
|
1.0
|
C21
|
A:QHL102
|
4.3
|
44.8
|
1.0
|
C11
|
A:QHL102
|
4.3
|
37.9
|
1.0
|
N11
|
A:QHL102
|
4.7
|
39.3
|
1.0
|
N7
|
A:QHL102
|
4.8
|
61.1
|
1.0
|
N10
|
A:QHL102
|
4.8
|
38.4
|
1.0
|
N6
|
A:QHL102
|
4.8
|
46.8
|
1.0
|
C4
|
A:QHL102
|
4.8
|
31.3
|
1.0
|
C9
|
A:QHL102
|
4.8
|
35.0
|
1.0
|
|
Ruthenium binding site 3 out
of 6 in 5ls8
Go back to
Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 3 out
of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 3 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ru101
b:35.9
occ:1.00
|
RU
|
B:QHL101
|
0.0
|
35.9
|
1.0
|
N9
|
B:QHL101
|
1.8
|
33.3
|
1.0
|
N12
|
B:QHL101
|
1.8
|
39.4
|
1.0
|
N1
|
B:QHL101
|
1.8
|
37.4
|
1.0
|
N5
|
B:QHL101
|
1.8
|
39.4
|
1.0
|
N8
|
B:QHL101
|
1.8
|
46.1
|
1.0
|
N2
|
B:QHL101
|
1.8
|
38.8
|
1.0
|
C29
|
B:QHL101
|
2.7
|
37.3
|
1.0
|
C36
|
B:QHL101
|
2.7
|
41.5
|
1.0
|
C10
|
B:QHL101
|
2.7
|
44.2
|
1.0
|
C1
|
B:QHL101
|
2.7
|
35.9
|
1.0
|
C26
|
B:QHL101
|
2.7
|
37.9
|
1.0
|
C19
|
B:QHL101
|
2.7
|
46.7
|
1.0
|
C30
|
B:QHL101
|
2.8
|
42.8
|
1.0
|
C12
|
B:QHL101
|
2.9
|
44.1
|
1.0
|
C38
|
B:QHL101
|
2.9
|
42.7
|
1.0
|
C28
|
B:QHL101
|
2.9
|
40.1
|
1.0
|
C20
|
B:QHL101
|
2.9
|
43.6
|
1.0
|
C2
|
B:QHL101
|
2.9
|
37.8
|
1.0
|
C32
|
B:QHL101
|
4.0
|
41.4
|
1.0
|
C35
|
B:QHL101
|
4.0
|
38.9
|
1.0
|
C8
|
B:QHL101
|
4.1
|
41.7
|
1.0
|
C25
|
B:QHL101
|
4.1
|
45.5
|
1.0
|
C22
|
B:QHL101
|
4.1
|
41.6
|
1.0
|
C5
|
B:QHL101
|
4.1
|
32.4
|
1.0
|
C31
|
B:QHL101
|
4.1
|
47.8
|
1.0
|
C11
|
B:QHL101
|
4.1
|
44.8
|
1.0
|
C37
|
B:QHL101
|
4.1
|
43.8
|
1.0
|
C27
|
B:QHL101
|
4.1
|
47.4
|
1.0
|
C21
|
B:QHL101
|
4.1
|
41.0
|
1.0
|
C3
|
B:QHL101
|
4.2
|
33.6
|
1.0
|
N10
|
B:QHL101
|
4.6
|
44.8
|
1.0
|
N11
|
B:QHL101
|
4.6
|
41.0
|
1.0
|
N7
|
B:QHL101
|
4.6
|
41.6
|
1.0
|
C9
|
B:QHL101
|
4.6
|
46.3
|
1.0
|
N6
|
B:QHL101
|
4.6
|
39.2
|
1.0
|
C4
|
B:QHL101
|
4.7
|
34.6
|
1.0
|
O4'
|
D:DG3
|
4.8
|
39.7
|
1.0
|
O
|
B:HOH203
|
4.9
|
46.7
|
1.0
|
|
Ruthenium binding site 4 out
of 6 in 5ls8
Go back to
Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 4 out
of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 4 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ru101
b:39.1
occ:1.00
|
RU
|
C:QHL101
|
0.0
|
39.1
|
1.0
|
N9
|
C:QHL101
|
1.8
|
37.7
|
1.0
|
N8
|
C:QHL101
|
1.8
|
49.8
|
1.0
|
N12
|
C:QHL101
|
1.8
|
43.2
|
1.0
|
N5
|
C:QHL101
|
1.8
|
51.0
|
1.0
|
N1
|
C:QHL101
|
1.8
|
37.7
|
1.0
|
N2
|
C:QHL101
|
1.9
|
43.6
|
1.0
|
C26
|
C:QHL101
|
2.7
|
46.9
|
1.0
|
C19
|
C:QHL101
|
2.7
|
51.6
|
1.0
|
C29
|
C:QHL101
|
2.7
|
44.0
|
1.0
|
C36
|
C:QHL101
|
2.7
|
37.7
|
1.0
|
C10
|
C:QHL101
|
2.8
|
36.2
|
1.0
|
C1
|
C:QHL101
|
2.8
|
36.0
|
1.0
|
C30
|
C:QHL101
|
2.9
|
44.1
|
1.0
|
C12
|
C:QHL101
|
2.9
|
44.5
|
1.0
|
C28
|
C:QHL101
|
2.9
|
50.3
|
1.0
|
C38
|
C:QHL101
|
2.9
|
40.2
|
1.0
|
C20
|
C:QHL101
|
2.9
|
44.5
|
1.0
|
C2
|
C:QHL101
|
2.9
|
34.4
|
1.0
|
C25
|
C:QHL101
|
4.0
|
52.8
|
1.0
|
C32
|
C:QHL101
|
4.0
|
39.7
|
1.0
|
C22
|
C:QHL101
|
4.0
|
56.0
|
1.0
|
C35
|
C:QHL101
|
4.1
|
46.0
|
1.0
|
C8
|
C:QHL101
|
4.1
|
36.8
|
1.0
|
C27
|
C:QHL101
|
4.1
|
46.5
|
1.0
|
C31
|
C:QHL101
|
4.1
|
36.8
|
1.0
|
C5
|
C:QHL101
|
4.1
|
23.0
|
1.0
|
C11
|
C:QHL101
|
4.1
|
41.4
|
1.0
|
C37
|
C:QHL101
|
4.1
|
46.1
|
1.0
|
C21
|
C:QHL101
|
4.1
|
52.5
|
1.0
|
C3
|
C:QHL101
|
4.2
|
34.2
|
1.0
|
N7
|
C:QHL101
|
4.6
|
47.3
|
1.0
|
N10
|
C:QHL101
|
4.6
|
40.8
|
1.0
|
N6
|
C:QHL101
|
4.6
|
50.8
|
1.0
|
N11
|
C:QHL101
|
4.6
|
40.6
|
1.0
|
C9
|
C:QHL101
|
4.7
|
40.1
|
1.0
|
O4'
|
A:DG3
|
4.7
|
39.0
|
1.0
|
C4
|
C:QHL101
|
4.7
|
31.4
|
1.0
|
O
|
C:HOH203
|
4.8
|
51.7
|
1.0
|
|
Ruthenium binding site 5 out
of 6 in 5ls8
Go back to
Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 5 out
of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 5 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ru102
b:38.1
occ:1.00
|
RU
|
C:QHL102
|
0.0
|
38.1
|
1.0
|
N12
|
C:QHL102
|
2.0
|
36.9
|
1.0
|
N2
|
C:QHL102
|
2.0
|
25.5
|
1.0
|
N9
|
C:QHL102
|
2.0
|
40.8
|
1.0
|
N1
|
C:QHL102
|
2.0
|
36.8
|
1.0
|
N8
|
C:QHL102
|
2.1
|
44.8
|
1.0
|
N5
|
C:QHL102
|
2.1
|
36.3
|
1.0
|
C36
|
C:QHL102
|
2.9
|
41.9
|
1.0
|
C29
|
C:QHL102
|
2.9
|
39.0
|
1.0
|
C1
|
C:QHL102
|
2.9
|
36.0
|
1.0
|
C10
|
C:QHL102
|
2.9
|
34.6
|
1.0
|
C19
|
C:QHL102
|
2.9
|
51.0
|
1.0
|
C26
|
C:QHL102
|
2.9
|
54.5
|
1.0
|
C38
|
C:QHL102
|
3.0
|
41.7
|
1.0
|
C2
|
C:QHL102
|
3.0
|
33.8
|
1.0
|
C12
|
C:QHL102
|
3.0
|
42.1
|
1.0
|
C28
|
C:QHL102
|
3.1
|
56.8
|
1.0
|
C30
|
C:QHL102
|
3.1
|
40.4
|
1.0
|
C20
|
C:QHL102
|
3.1
|
45.1
|
1.0
|
C35
|
C:QHL102
|
4.2
|
35.2
|
1.0
|
C32
|
C:QHL102
|
4.2
|
36.9
|
1.0
|
C5
|
C:QHL102
|
4.2
|
32.3
|
1.0
|
C8
|
C:QHL102
|
4.2
|
31.6
|
1.0
|
C22
|
C:QHL102
|
4.2
|
46.5
|
1.0
|
C25
|
C:QHL102
|
4.2
|
57.0
|
1.0
|
C37
|
C:QHL102
|
4.3
|
39.9
|
1.0
|
C3
|
C:QHL102
|
4.3
|
35.5
|
1.0
|
C11
|
C:QHL102
|
4.3
|
39.2
|
1.0
|
C31
|
C:QHL102
|
4.3
|
40.3
|
1.0
|
C27
|
C:QHL102
|
4.3
|
61.2
|
1.0
|
C21
|
C:QHL102
|
4.3
|
48.6
|
1.0
|
N11
|
C:QHL102
|
4.7
|
43.1
|
1.0
|
N10
|
C:QHL102
|
4.7
|
38.8
|
1.0
|
C4
|
C:QHL102
|
4.8
|
31.1
|
1.0
|
N7
|
C:QHL102
|
4.8
|
57.2
|
1.0
|
N6
|
C:QHL102
|
4.8
|
51.0
|
1.0
|
C9
|
C:QHL102
|
4.8
|
34.6
|
1.0
|
C16
|
A:QHL102
|
5.0
|
38.7
|
1.0
|
|
Ruthenium binding site 6 out
of 6 in 5ls8
Go back to
Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 6 out
of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 6 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ru101
b:36.5
occ:1.00
|
RU
|
D:QHL101
|
0.0
|
36.5
|
1.0
|
N9
|
D:QHL101
|
1.8
|
35.0
|
1.0
|
N1
|
D:QHL101
|
1.8
|
38.8
|
1.0
|
N12
|
D:QHL101
|
1.8
|
42.0
|
1.0
|
N5
|
D:QHL101
|
1.8
|
38.2
|
1.0
|
N8
|
D:QHL101
|
1.8
|
47.5
|
1.0
|
N2
|
D:QHL101
|
1.8
|
36.4
|
1.0
|
C29
|
D:QHL101
|
2.7
|
36.1
|
1.0
|
C36
|
D:QHL101
|
2.7
|
41.2
|
1.0
|
C10
|
D:QHL101
|
2.7
|
39.9
|
1.0
|
C1
|
D:QHL101
|
2.7
|
38.1
|
1.0
|
C19
|
D:QHL101
|
2.7
|
45.5
|
1.0
|
C26
|
D:QHL101
|
2.7
|
40.5
|
1.0
|
C30
|
D:QHL101
|
2.8
|
42.0
|
1.0
|
C12
|
D:QHL101
|
2.8
|
46.0
|
1.0
|
C38
|
D:QHL101
|
2.9
|
43.9
|
1.0
|
C20
|
D:QHL101
|
2.9
|
41.2
|
1.0
|
C28
|
D:QHL101
|
2.9
|
42.5
|
1.0
|
C2
|
D:QHL101
|
2.9
|
32.0
|
1.0
|
C32
|
D:QHL101
|
4.0
|
39.6
|
1.0
|
C35
|
D:QHL101
|
4.0
|
43.7
|
1.0
|
C8
|
D:QHL101
|
4.0
|
40.6
|
1.0
|
C5
|
D:QHL101
|
4.1
|
22.6
|
1.0
|
C22
|
D:QHL101
|
4.1
|
41.9
|
1.0
|
C25
|
D:QHL101
|
4.1
|
48.0
|
1.0
|
C31
|
D:QHL101
|
4.1
|
48.0
|
1.0
|
C11
|
D:QHL101
|
4.1
|
39.3
|
1.0
|
C37
|
D:QHL101
|
4.1
|
46.6
|
1.0
|
C21
|
D:QHL101
|
4.1
|
39.5
|
1.0
|
C27
|
D:QHL101
|
4.1
|
50.5
|
1.0
|
C3
|
D:QHL101
|
4.2
|
30.9
|
1.0
|
N10
|
D:QHL101
|
4.6
|
46.1
|
1.0
|
N11
|
D:QHL101
|
4.6
|
45.4
|
1.0
|
C9
|
D:QHL101
|
4.6
|
45.9
|
1.0
|
N6
|
D:QHL101
|
4.6
|
39.3
|
1.0
|
N7
|
D:QHL101
|
4.6
|
43.3
|
1.0
|
C4
|
D:QHL101
|
4.7
|
29.5
|
1.0
|
O4'
|
B:DG3
|
4.9
|
41.3
|
1.0
|
|
Reference:
K.Mcquaid,
H.Abell,
S.P.Gurung,
D.R.Allan,
G.Winter,
T.Sorensen,
D.J.Cardin,
J.A.Brazier,
C.J.Cardin,
J.P.Hall.
Structural Studies Reveal Enantiospecific Recognition of A Dna G-Quadruplex By A Ruthenium Polypyridyl Complex. Angew.Chem.Int.Ed.Engl. V. 58 9881 2019.
ISSN: ESSN 1521-3773
PubMed: 30958918
DOI: 10.1002/ANIE.201814502
Page generated: Thu Oct 10 13:00:44 2024
|