Ruthenium in PDB 8cmm: Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide
Protein crystallography data
The structure of Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide, PDB code: 8cmm
was solved by
T.D.Prieto Otoya,
C.J.Cardin,
K.M.Mcquaid,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.20 /
0.90
|
Space group
|
I 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
31.395,
48.645,
54.192,
90,
90,
90
|
R / Rfree (%)
|
16.8 /
19
|
Ruthenium Binding Sites:
The binding sites of Ruthenium atom in the Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide
(pdb code 8cmm). This binding sites where shown within
5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the
Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide, PDB code: 8cmm:
Jump to Ruthenium binding site number:
1;
2;
Ruthenium binding site 1 out
of 2 in 8cmm
Go back to
Ruthenium Binding Sites List in 8cmm
Ruthenium binding site 1 out
of 2 in the Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 1 of Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru101
b:9.7
occ:0.46
|
RU01
|
A:V70101
|
0.0
|
9.7
|
0.5
|
N04
|
A:V70101
|
2.0
|
9.5
|
0.5
|
N02
|
A:V70101
|
2.0
|
11.1
|
0.5
|
N06
|
A:V70101
|
2.1
|
11.7
|
0.5
|
N03
|
A:V70101
|
2.1
|
11.4
|
0.5
|
N05
|
A:V70101
|
2.1
|
12.6
|
0.5
|
N01
|
A:V70101
|
2.1
|
10.6
|
0.5
|
H24
|
A:V70101
|
2.4
|
9.4
|
0.5
|
H26
|
A:V70101
|
2.7
|
9.6
|
0.5
|
C03
|
A:V70101
|
2.9
|
11.0
|
0.5
|
C01
|
A:V70101
|
2.9
|
12.0
|
0.5
|
C08
|
A:V70101
|
2.9
|
11.1
|
0.5
|
C07
|
A:V70101
|
2.9
|
10.9
|
0.5
|
C04
|
A:V70101
|
2.9
|
11.0
|
0.5
|
C10
|
A:V70101
|
2.9
|
10.0
|
0.5
|
C20
|
A:V70101
|
3.0
|
10.7
|
0.5
|
C12
|
A:V70101
|
3.1
|
13.9
|
0.5
|
C22
|
A:V70101
|
3.1
|
11.6
|
0.5
|
C19
|
A:V70101
|
3.1
|
12.4
|
0.5
|
H07
|
A:V70101
|
3.1
|
10.4
|
0.5
|
H03
|
A:V70101
|
3.2
|
11.6
|
0.5
|
H09
|
A:V70101
|
3.2
|
10.5
|
0.5
|
H06
|
A:V70101
|
3.2
|
11.6
|
0.5
|
O
|
A:HOH242
|
4.0
|
19.7
|
1.0
|
H21
|
A:V7F102
|
4.0
|
9.7
|
0.8
|
H15
|
A:V7F102
|
4.2
|
9.6
|
0.0
|
C11
|
A:V70101
|
4.3
|
13.4
|
0.5
|
C02
|
A:V70101
|
4.3
|
11.0
|
0.5
|
C17
|
A:V70101
|
4.3
|
12.6
|
0.5
|
C23
|
A:V70101
|
4.3
|
10.7
|
0.5
|
C13
|
A:V70101
|
4.3
|
12.0
|
0.5
|
C14
|
A:V70101
|
4.3
|
10.0
|
0.5
|
C05
|
A:V70101
|
4.3
|
12.5
|
0.5
|
C21
|
A:V70101
|
4.4
|
15.0
|
0.5
|
C34
|
A:V70101
|
4.4
|
13.2
|
0.5
|
C15
|
A:V70101
|
4.4
|
12.8
|
0.5
|
H05
|
A:V70101
|
4.6
|
9.7
|
0.5
|
H25
|
A:V70101
|
4.6
|
10.0
|
0.5
|
C25
|
A:V70101
|
4.8
|
14.8
|
0.5
|
C36
|
A:V7F102
|
4.8
|
11.3
|
1.0
|
C24
|
A:V70101
|
4.8
|
12.8
|
0.5
|
C33
|
A:V70101
|
4.9
|
12.9
|
0.5
|
C06
|
A:V70101
|
4.9
|
14.6
|
0.5
|
C18
|
A:V70101
|
4.9
|
11.9
|
0.5
|
C30
|
A:V7F102
|
4.9
|
10.6
|
1.0
|
|
Ruthenium binding site 2 out
of 2 in 8cmm
Go back to
Ruthenium Binding Sites List in 8cmm
Ruthenium binding site 2 out
of 2 in the Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 2 of Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru102
b:9.9
occ:1.00
|
RU01
|
A:V7F102
|
0.0
|
9.9
|
1.0
|
N04
|
A:V7F102
|
2.0
|
9.3
|
1.0
|
N02
|
A:V7F102
|
2.0
|
9.5
|
1.0
|
N06
|
A:V7F102
|
2.1
|
10.3
|
1.0
|
N05
|
A:V7F102
|
2.1
|
9.9
|
1.0
|
N01
|
A:V7F102
|
2.1
|
10.1
|
1.0
|
N03
|
A:V7F102
|
2.1
|
9.4
|
1.0
|
H24
|
A:V7F102
|
2.4
|
9.5
|
1.0
|
H26
|
A:V7F102
|
2.7
|
10.1
|
0.9
|
C03
|
A:V7F102
|
2.9
|
9.2
|
1.0
|
C07
|
A:V7F102
|
2.9
|
9.4
|
1.0
|
C08
|
A:V7F102
|
2.9
|
8.8
|
1.0
|
C04
|
A:V7F102
|
2.9
|
9.6
|
1.0
|
C10
|
A:V7F102
|
2.9
|
9.6
|
1.0
|
C01
|
A:V7F102
|
2.9
|
9.7
|
1.0
|
C22
|
A:V7F102
|
3.1
|
10.3
|
1.0
|
C20
|
A:V7F102
|
3.1
|
10.4
|
1.0
|
C19
|
A:V7F102
|
3.1
|
10.2
|
1.0
|
C12
|
A:V7F102
|
3.1
|
9.9
|
1.0
|
H09
|
A:V7F102
|
3.2
|
9.4
|
0.0
|
H07
|
A:V7F102
|
3.2
|
8.7
|
0.9
|
H06
|
A:V7F102
|
3.2
|
9.2
|
0.9
|
H03
|
A:V7F102
|
3.2
|
8.0
|
1.0
|
C17
|
A:V7F102
|
4.3
|
10.0
|
1.0
|
C23
|
A:V7F102
|
4.3
|
10.3
|
1.0
|
C13
|
A:V7F102
|
4.3
|
10.0
|
1.0
|
C02
|
A:V7F102
|
4.3
|
9.5
|
1.0
|
C11
|
A:V7F102
|
4.3
|
9.6
|
1.0
|
C14
|
A:V7F102
|
4.3
|
9.3
|
1.0
|
C34
|
A:V7F102
|
4.4
|
10.3
|
1.0
|
C05
|
A:V7F102
|
4.4
|
10.3
|
1.0
|
C21
|
A:V7F102
|
4.4
|
11.6
|
1.0
|
C15
|
A:V7F102
|
4.4
|
10.7
|
1.0
|
O
|
A:HOH237
|
4.5
|
13.6
|
1.0
|
H25
|
A:V7F102
|
4.6
|
9.8
|
0.0
|
H05
|
A:V7F102
|
4.6
|
7.2
|
1.0
|
H2
|
A:DA5
|
4.7
|
8.8
|
1.0
|
H23
|
A:V70101
|
4.8
|
10.2
|
0.5
|
C33
|
A:V7F102
|
4.8
|
10.4
|
1.0
|
C06
|
A:V7F102
|
4.9
|
10.6
|
1.0
|
C24
|
A:V7F102
|
4.9
|
11.5
|
1.0
|
C25
|
A:V7F102
|
4.9
|
11.0
|
1.0
|
C18
|
A:V7F102
|
4.9
|
10.2
|
1.0
|
C2
|
A:DA5
|
4.9
|
11.6
|
1.0
|
N3
|
A:DA5
|
5.0
|
11.1
|
1.0
|
C26
|
A:V7F102
|
5.0
|
10.0
|
1.0
|
|
Reference:
T.D.Prieto Otoya,
C.J.Cardin,
K.M.Mcquaid.
Ruthenium Polypyridyl Complexes Bound to Dna Mismatch Oligonucleotide To Be Published.
Page generated: Thu Oct 10 13:11:04 2024
|