Ruthenium in PDB 4e1u: [Ru(Bpy)2 Dppz]2+ Bound to Dna
Protein crystallography data
The structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna, PDB code: 4e1u
was solved by
H.Song,
J.T.Kaiser,
J.K.Barton,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.33 /
0.92
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
24.039,
24.797,
37.521,
74.67,
84.42,
76.21
|
R / Rfree (%)
|
14 /
14.9
|
Other elements in 4e1u:
The structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna also contains other interesting chemical elements:
Ruthenium Binding Sites:
The binding sites of Ruthenium atom in the [Ru(Bpy)2 Dppz]2+ Bound to Dna
(pdb code 4e1u). This binding sites where shown within
5.0 Angstroms radius around Ruthenium atom.
In total 5 binding sites of Ruthenium where determined in the
[Ru(Bpy)2 Dppz]2+ Bound to Dna, PDB code: 4e1u:
Jump to Ruthenium binding site number:
1;
2;
3;
4;
5;
Ruthenium binding site 1 out
of 5 in 4e1u
Go back to
Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 1 out
of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 1 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru101
b:16.0
occ:1.00
|
RU1
|
A:R1Z101
|
0.0
|
16.0
|
1.0
|
N1
|
A:R1Z101
|
1.9
|
14.6
|
1.0
|
N5
|
A:R1Z101
|
2.0
|
16.0
|
1.0
|
N6
|
A:R1Z101
|
2.0
|
16.9
|
1.0
|
N8
|
A:R1Z101
|
2.0
|
13.0
|
1.0
|
N2
|
A:R1Z101
|
2.1
|
14.6
|
1.0
|
N7
|
A:R1Z101
|
2.1
|
17.3
|
1.0
|
C2
|
A:R1Z101
|
2.7
|
15.6
|
1.0
|
C3
|
A:R1Z101
|
2.8
|
14.6
|
1.0
|
C24
|
A:R1Z101
|
2.8
|
17.4
|
1.0
|
C23
|
A:R1Z101
|
2.9
|
17.3
|
1.0
|
C33
|
A:R1Z101
|
2.9
|
16.7
|
1.0
|
C15
|
A:R1Z101
|
2.9
|
17.8
|
1.0
|
C34
|
A:R1Z101
|
2.9
|
15.1
|
1.0
|
C19
|
A:R1Z101
|
3.0
|
17.5
|
1.0
|
C38
|
A:R1Z101
|
3.0
|
12.8
|
1.0
|
C16
|
A:R1Z101
|
3.1
|
14.5
|
1.0
|
H151
|
A:R1Z101
|
3.1
|
21.3
|
1.0
|
C29
|
A:R1Z101
|
3.1
|
18.9
|
1.0
|
C28
|
A:R1Z101
|
3.1
|
17.3
|
1.0
|
H381
|
A:R1Z101
|
3.1
|
15.4
|
1.0
|
H191
|
A:R1Z101
|
3.2
|
21.0
|
1.0
|
H291
|
A:R1Z101
|
3.2
|
22.7
|
1.0
|
H161
|
A:R1Z101
|
3.2
|
17.4
|
1.0
|
H281
|
A:R1Z101
|
3.3
|
20.7
|
1.0
|
C1
|
A:R1Z101
|
4.1
|
17.0
|
1.0
|
C4
|
A:R1Z101
|
4.2
|
14.4
|
1.0
|
C22
|
A:R1Z101
|
4.2
|
19.5
|
1.0
|
C25
|
A:R1Z101
|
4.2
|
19.0
|
1.0
|
C14
|
A:R1Z101
|
4.2
|
19.4
|
1.0
|
C35
|
A:R1Z101
|
4.3
|
15.1
|
1.0
|
C32
|
A:R1Z101
|
4.3
|
19.9
|
1.0
|
C20
|
A:R1Z101
|
4.4
|
19.2
|
1.0
|
C17
|
A:R1Z101
|
4.4
|
14.0
|
1.0
|
C37
|
A:R1Z101
|
4.4
|
14.2
|
1.0
|
C30
|
A:R1Z101
|
4.4
|
19.9
|
1.0
|
C27
|
A:R1Z101
|
4.4
|
18.7
|
1.0
|
H21
|
A:DG2
|
4.7
|
14.3
|
1.0
|
C13
|
A:R1Z101
|
4.7
|
18.6
|
1.0
|
C21
|
A:R1Z101
|
4.8
|
18.9
|
1.0
|
C18
|
A:R1Z101
|
4.8
|
13.5
|
1.0
|
O
|
A:HOH224
|
4.8
|
27.7
|
1.0
|
C26
|
A:R1Z101
|
4.8
|
19.6
|
1.0
|
C36
|
A:R1Z101
|
4.8
|
14.2
|
1.0
|
C31
|
A:R1Z101
|
4.9
|
20.2
|
1.0
|
H221
|
A:R1Z101
|
5.0
|
23.4
|
1.0
|
H251
|
A:R1Z101
|
5.0
|
22.8
|
1.0
|
|
Ruthenium binding site 2 out
of 5 in 4e1u
Go back to
Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 2 out
of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 2 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru102
b:12.6
occ:1.00
|
RU1
|
A:R1Z102
|
0.0
|
12.6
|
1.0
|
N8
|
A:R1Z102
|
2.0
|
13.5
|
1.0
|
N5
|
A:R1Z102
|
2.0
|
12.9
|
1.0
|
N2
|
A:R1Z102
|
2.1
|
12.6
|
1.0
|
N6
|
A:R1Z102
|
2.1
|
13.3
|
1.0
|
N1
|
A:R1Z102
|
2.1
|
12.4
|
1.0
|
N7
|
A:R1Z102
|
2.1
|
14.7
|
1.0
|
C34
|
A:R1Z102
|
2.9
|
13.6
|
1.0
|
C2
|
A:R1Z102
|
2.9
|
12.3
|
1.0
|
C3
|
A:R1Z102
|
2.9
|
12.3
|
1.0
|
C23
|
A:R1Z102
|
2.9
|
14.4
|
1.0
|
C24
|
A:R1Z102
|
2.9
|
14.2
|
1.0
|
C33
|
A:R1Z102
|
2.9
|
14.0
|
1.0
|
C38
|
A:R1Z102
|
3.0
|
14.2
|
1.0
|
C19
|
A:R1Z102
|
3.0
|
13.9
|
1.0
|
C16
|
A:R1Z102
|
3.1
|
13.2
|
1.0
|
C15
|
A:R1Z102
|
3.1
|
12.4
|
1.0
|
C28
|
A:R1Z102
|
3.1
|
14.2
|
1.0
|
C29
|
A:R1Z102
|
3.1
|
15.4
|
1.0
|
H191
|
A:R1Z102
|
3.2
|
16.6
|
1.0
|
H161
|
A:R1Z102
|
3.2
|
15.9
|
1.0
|
H381
|
A:R1Z102
|
3.2
|
17.0
|
1.0
|
H151
|
A:R1Z102
|
3.2
|
14.9
|
1.0
|
H281
|
A:R1Z102
|
3.2
|
17.0
|
1.0
|
H291
|
A:R1Z102
|
3.3
|
18.5
|
1.0
|
C35
|
A:R1Z102
|
4.2
|
15.6
|
1.0
|
C22
|
A:R1Z102
|
4.2
|
15.4
|
1.0
|
C4
|
A:R1Z102
|
4.3
|
13.3
|
1.0
|
C1
|
A:R1Z102
|
4.3
|
12.9
|
1.0
|
C25
|
A:R1Z102
|
4.3
|
15.5
|
1.0
|
C32
|
A:R1Z102
|
4.3
|
14.9
|
1.0
|
C17
|
A:R1Z102
|
4.4
|
14.2
|
1.0
|
C14
|
A:R1Z102
|
4.4
|
13.4
|
1.0
|
C37
|
A:R1Z102
|
4.4
|
16.1
|
1.0
|
C27
|
A:R1Z102
|
4.4
|
15.9
|
1.0
|
C20
|
A:R1Z102
|
4.4
|
15.2
|
1.0
|
C30
|
A:R1Z102
|
4.4
|
15.8
|
1.0
|
C36
|
A:R1Z102
|
4.8
|
15.7
|
1.0
|
C21
|
A:R1Z102
|
4.8
|
16.0
|
1.0
|
C18
|
A:R1Z102
|
4.8
|
13.7
|
1.0
|
C26
|
A:R1Z102
|
4.9
|
15.8
|
1.0
|
C13
|
A:R1Z102
|
4.9
|
13.3
|
1.0
|
C31
|
A:R1Z102
|
4.9
|
15.2
|
1.0
|
H21
|
A:DG3
|
4.9
|
14.0
|
0.8
|
H21
|
A:DG3
|
4.9
|
16.9
|
0.2
|
H351
|
A:R1Z102
|
5.0
|
18.8
|
1.0
|
|
Ruthenium binding site 3 out
of 5 in 4e1u
Go back to
Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 3 out
of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 3 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru103
b:10.3
occ:1.00
|
RU1
|
A:R1Z103
|
0.0
|
10.3
|
1.0
|
N5
|
A:R1Z103
|
2.0
|
10.0
|
1.0
|
N8
|
A:R1Z103
|
2.0
|
11.8
|
1.0
|
N1
|
A:R1Z103
|
2.0
|
10.2
|
1.0
|
N2
|
A:R1Z103
|
2.1
|
10.1
|
1.0
|
N7
|
A:R1Z103
|
2.1
|
10.9
|
1.0
|
N6
|
A:R1Z103
|
2.1
|
11.1
|
1.0
|
C2
|
A:R1Z103
|
2.9
|
10.0
|
1.0
|
C3
|
A:R1Z103
|
2.9
|
9.7
|
1.0
|
C33
|
A:R1Z103
|
2.9
|
11.4
|
1.0
|
C24
|
A:R1Z103
|
2.9
|
11.4
|
1.0
|
C34
|
A:R1Z103
|
2.9
|
12.1
|
1.0
|
C23
|
A:R1Z103
|
2.9
|
10.6
|
1.0
|
C19
|
A:R1Z103
|
3.0
|
10.3
|
1.0
|
C38
|
A:R1Z103
|
3.0
|
13.2
|
1.0
|
C15
|
A:R1Z103
|
3.0
|
10.5
|
1.0
|
C28
|
A:R1Z103
|
3.0
|
12.8
|
1.0
|
C16
|
A:R1Z103
|
3.1
|
11.2
|
1.0
|
C29
|
A:R1Z103
|
3.1
|
11.1
|
1.0
|
H191
|
A:R1Z103
|
3.1
|
12.3
|
1.0
|
H381
|
A:R1Z103
|
3.1
|
15.9
|
1.0
|
H151
|
A:R1Z103
|
3.1
|
12.7
|
1.0
|
H281
|
A:R1Z103
|
3.1
|
15.3
|
1.0
|
H161
|
A:R1Z103
|
3.2
|
13.4
|
1.0
|
H291
|
A:R1Z103
|
3.2
|
13.3
|
1.0
|
C4
|
A:R1Z103
|
4.2
|
11.2
|
1.0
|
C1
|
A:R1Z103
|
4.2
|
10.4
|
1.0
|
C35
|
A:R1Z103
|
4.2
|
15.8
|
1.0
|
C32
|
A:R1Z103
|
4.2
|
13.0
|
1.0
|
C22
|
A:R1Z103
|
4.3
|
11.9
|
1.0
|
C25
|
A:R1Z103
|
4.3
|
13.6
|
1.0
|
C14
|
A:R1Z103
|
4.3
|
11.3
|
1.0
|
C27
|
A:R1Z103
|
4.3
|
15.3
|
1.0
|
C30
|
A:R1Z103
|
4.3
|
11.6
|
1.0
|
C17
|
A:R1Z103
|
4.3
|
11.6
|
1.0
|
C20
|
A:R1Z103
|
4.4
|
10.9
|
1.0
|
C37
|
A:R1Z103
|
4.4
|
14.9
|
1.0
|
C18
|
A:R1Z103
|
4.8
|
12.0
|
1.0
|
C13
|
A:R1Z103
|
4.8
|
10.5
|
1.0
|
C26
|
A:R1Z103
|
4.8
|
16.0
|
1.0
|
C31
|
A:R1Z103
|
4.8
|
13.1
|
1.0
|
C36
|
A:R1Z103
|
4.8
|
15.8
|
1.0
|
C21
|
A:R1Z103
|
4.9
|
12.2
|
1.0
|
O
|
B:HOH1026
|
4.9
|
28.6
|
1.0
|
O
|
A:HOH245
|
4.9
|
29.2
|
1.0
|
H62
|
B:DA9
|
4.9
|
16.6
|
1.0
|
H62
|
A:DA9
|
5.0
|
15.0
|
1.0
|
|
Ruthenium binding site 4 out
of 5 in 4e1u
Go back to
Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 4 out
of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 4 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru104
b:9.7
occ:1.00
|
RU1
|
A:R1Z104
|
0.0
|
9.7
|
1.0
|
N7
|
A:R1Z104
|
2.0
|
11.1
|
1.0
|
N5
|
A:R1Z104
|
2.0
|
9.6
|
1.0
|
N6
|
A:R1Z104
|
2.1
|
10.4
|
1.0
|
N1
|
A:R1Z104
|
2.1
|
9.8
|
1.0
|
N2
|
A:R1Z104
|
2.1
|
9.4
|
1.0
|
N8
|
A:R1Z104
|
2.1
|
11.2
|
1.0
|
C2
|
A:R1Z104
|
2.9
|
9.6
|
1.0
|
C3
|
A:R1Z104
|
2.9
|
9.4
|
1.0
|
C24
|
A:R1Z104
|
2.9
|
10.0
|
1.0
|
C33
|
A:R1Z104
|
2.9
|
13.0
|
1.0
|
C23
|
A:R1Z104
|
2.9
|
9.8
|
1.0
|
C34
|
A:R1Z104
|
3.0
|
12.9
|
1.0
|
C29
|
A:R1Z104
|
3.0
|
12.6
|
1.0
|
C19
|
A:R1Z104
|
3.0
|
9.7
|
1.0
|
C28
|
A:R1Z104
|
3.1
|
11.4
|
1.0
|
C15
|
A:R1Z104
|
3.1
|
10.7
|
1.0
|
C38
|
A:R1Z104
|
3.1
|
11.9
|
1.0
|
C16
|
A:R1Z104
|
3.1
|
10.2
|
1.0
|
H291
|
A:R1Z104
|
3.1
|
15.1
|
1.0
|
H191
|
A:R1Z104
|
3.1
|
11.6
|
1.0
|
H281
|
A:R1Z104
|
3.2
|
13.7
|
1.0
|
H151
|
A:R1Z104
|
3.2
|
12.9
|
1.0
|
H161
|
A:R1Z104
|
3.2
|
12.2
|
1.0
|
H381
|
A:R1Z104
|
3.2
|
14.2
|
1.0
|
C1
|
A:R1Z104
|
4.2
|
10.0
|
1.0
|
C22
|
A:R1Z104
|
4.2
|
11.5
|
1.0
|
C25
|
A:R1Z104
|
4.2
|
11.4
|
1.0
|
C32
|
A:R1Z104
|
4.2
|
14.9
|
1.0
|
C4
|
A:R1Z104
|
4.3
|
9.8
|
1.0
|
C35
|
A:R1Z104
|
4.3
|
15.3
|
1.0
|
C30
|
A:R1Z104
|
4.3
|
14.5
|
1.0
|
C27
|
A:R1Z104
|
4.4
|
12.5
|
1.0
|
C14
|
A:R1Z104
|
4.4
|
10.5
|
1.0
|
C20
|
A:R1Z104
|
4.4
|
10.4
|
1.0
|
C17
|
A:R1Z104
|
4.4
|
10.2
|
1.0
|
C37
|
A:R1Z104
|
4.4
|
14.9
|
1.0
|
H1'
|
B:DA5
|
4.5
|
16.2
|
0.2
|
H2
|
B:DA4
|
4.6
|
12.7
|
1.0
|
H21
|
B:DG3
|
4.6
|
11.0
|
0.5
|
H21
|
B:DG3
|
4.7
|
11.2
|
0.5
|
H1'
|
B:DA5
|
4.8
|
15.5
|
0.8
|
C31
|
A:R1Z104
|
4.8
|
16.0
|
1.0
|
C13
|
A:R1Z104
|
4.8
|
10.7
|
1.0
|
C26
|
A:R1Z104
|
4.8
|
12.0
|
1.0
|
C21
|
A:R1Z104
|
4.8
|
10.2
|
1.0
|
C18
|
A:R1Z104
|
4.9
|
10.3
|
1.0
|
O
|
B:HOH1016
|
4.9
|
25.1
|
1.0
|
C36
|
A:R1Z104
|
4.9
|
16.0
|
1.0
|
C2
|
B:DA4
|
4.9
|
10.6
|
1.0
|
H22
|
B:DG3
|
5.0
|
11.0
|
0.5
|
|
Ruthenium binding site 5 out
of 5 in 4e1u
Go back to
Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 5 out
of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 5 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru105
b:9.8
occ:1.00
|
RU1
|
A:R1Z105
|
0.0
|
9.8
|
1.0
|
N8
|
A:R1Z105
|
2.0
|
12.3
|
1.0
|
N5
|
A:R1Z105
|
2.0
|
10.7
|
1.0
|
N6
|
A:R1Z105
|
2.1
|
10.2
|
1.0
|
N7
|
A:R1Z105
|
2.1
|
11.0
|
1.0
|
N1
|
A:R1Z105
|
2.1
|
9.2
|
1.0
|
N2
|
A:R1Z105
|
2.1
|
10.0
|
1.0
|
C2
|
A:R1Z105
|
2.9
|
9.8
|
1.0
|
C24
|
A:R1Z105
|
2.9
|
10.8
|
1.0
|
C23
|
A:R1Z105
|
2.9
|
10.9
|
1.0
|
C33
|
A:R1Z105
|
2.9
|
11.8
|
1.0
|
C3
|
A:R1Z105
|
2.9
|
9.7
|
1.0
|
C34
|
A:R1Z105
|
2.9
|
13.2
|
1.0
|
C19
|
A:R1Z105
|
3.0
|
11.2
|
1.0
|
C38
|
A:R1Z105
|
3.0
|
14.2
|
1.0
|
C15
|
A:R1Z105
|
3.0
|
10.4
|
1.0
|
C29
|
A:R1Z105
|
3.0
|
10.7
|
1.0
|
C28
|
A:R1Z105
|
3.1
|
10.8
|
1.0
|
C16
|
A:R1Z105
|
3.1
|
11.0
|
1.0
|
H191
|
A:R1Z105
|
3.1
|
13.4
|
1.0
|
H291
|
A:R1Z105
|
3.1
|
12.8
|
1.0
|
H151
|
A:R1Z105
|
3.1
|
12.4
|
1.0
|
H381
|
A:R1Z105
|
3.2
|
17.1
|
1.0
|
H281
|
A:R1Z105
|
3.2
|
13.0
|
1.0
|
H161
|
A:R1Z105
|
3.2
|
13.2
|
1.0
|
C22
|
A:R1Z105
|
4.2
|
12.7
|
1.0
|
C25
|
A:R1Z105
|
4.3
|
12.3
|
1.0
|
C1
|
A:R1Z105
|
4.3
|
10.7
|
1.0
|
C35
|
A:R1Z105
|
4.3
|
16.1
|
1.0
|
C32
|
A:R1Z105
|
4.3
|
13.8
|
1.0
|
H21
|
B:DG2
|
4.3
|
12.2
|
0.5
|
C4
|
A:R1Z105
|
4.3
|
10.6
|
1.0
|
C14
|
A:R1Z105
|
4.3
|
11.8
|
1.0
|
C30
|
A:R1Z105
|
4.3
|
12.5
|
1.0
|
C27
|
A:R1Z105
|
4.3
|
11.5
|
1.0
|
C20
|
A:R1Z105
|
4.4
|
12.3
|
1.0
|
C17
|
A:R1Z105
|
4.4
|
11.3
|
1.0
|
C37
|
A:R1Z105
|
4.4
|
15.8
|
1.0
|
H21
|
B:DG2
|
4.6
|
12.1
|
0.6
|
C13
|
A:R1Z105
|
4.8
|
11.8
|
1.0
|
C26
|
A:R1Z105
|
4.8
|
12.6
|
1.0
|
C31
|
A:R1Z105
|
4.8
|
13.1
|
1.0
|
C21
|
A:R1Z105
|
4.8
|
12.7
|
1.0
|
C36
|
A:R1Z105
|
4.9
|
16.4
|
1.0
|
C18
|
A:R1Z105
|
4.9
|
11.4
|
1.0
|
N2
|
B:DG2
|
4.9
|
10.2
|
0.5
|
N3
|
B:DG2
|
4.9
|
11.6
|
0.5
|
|
Reference:
H.Song,
J.T.Kaiser,
J.K.Barton.
Crystal Structure of Delta-[Ru(Bpy)2DPPZ]2+ Bound to Mismatched Dna Reveals Side-By-Side Metalloinsertion and Intercalation. Nat Chem V. 4 615 2012.
ISSN: ISSN 1755-4349
PubMed: 22824892
DOI: 10.1038/NCHEM.1375
Page generated: Thu Oct 10 12:51:17 2024
|