Silver in PDB 7xkm: Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Protein crystallography data
The structure of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions, PDB code: 7xkm
was solved by
J.Kondo,
A.Ono,
T.Atsugi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.96 /
2.79
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.461,
77.461,
123.722,
90,
90,
120
|
R / Rfree (%)
|
18.7 /
21.7
|
Other elements in 7xkm:
The structure of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions also contains other interesting chemical elements:
Silver Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
23;
Binding sites:
The binding sites of Silver atom in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
(pdb code 7xkm). This binding sites where shown within
5.0 Angstroms radius around Silver atom.
In total 23 binding sites of Silver where determined in the
Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions, PDB code: 7xkm:
Jump to Silver binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Silver binding site 1 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 1 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 1 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag101
b:46.5
occ:1.00
|
N3
|
A:DC3
|
2.2
|
36.5
|
1.0
|
N3
|
B:DC9
|
2.2
|
36.7
|
1.0
|
O6
|
A:DG2
|
3.0
|
43.6
|
1.0
|
C2
|
A:DC3
|
3.0
|
38.9
|
1.0
|
O2
|
A:DC3
|
3.0
|
39.7
|
1.0
|
AG
|
A:AG102
|
3.0
|
45.2
|
1.0
|
C4
|
B:DC9
|
3.1
|
35.8
|
1.0
|
N4
|
B:DC9
|
3.1
|
35.8
|
1.0
|
AG
|
B:AG102
|
3.1
|
49.2
|
1.0
|
C2
|
B:DC9
|
3.1
|
42.7
|
1.0
|
C4
|
A:DC3
|
3.2
|
40.9
|
1.0
|
O2
|
B:DC9
|
3.3
|
47.1
|
1.0
|
N3
|
B:BRU8
|
3.3
|
34.1
|
1.0
|
N4
|
A:DC3
|
3.4
|
43.0
|
1.0
|
N7
|
B:DG10
|
3.6
|
38.9
|
1.0
|
O4
|
B:BRU8
|
3.6
|
38.5
|
1.0
|
C6
|
A:DG2
|
3.6
|
39.8
|
1.0
|
C4
|
B:BRU8
|
3.7
|
37.9
|
1.0
|
N7
|
A:DG4
|
3.9
|
39.5
|
1.0
|
O6
|
B:DG10
|
4.0
|
45.1
|
1.0
|
N7
|
A:DG2
|
4.0
|
39.9
|
1.0
|
C5
|
A:DG2
|
4.1
|
37.5
|
1.0
|
C5
|
B:DG10
|
4.1
|
41.0
|
1.0
|
C2
|
B:BRU8
|
4.3
|
35.4
|
1.0
|
C6
|
B:DG10
|
4.3
|
42.4
|
1.0
|
N1
|
A:DC3
|
4.3
|
42.5
|
1.0
|
C8
|
B:DG10
|
4.4
|
39.0
|
1.0
|
N1
|
B:DC9
|
4.4
|
42.2
|
1.0
|
C5
|
B:DC9
|
4.5
|
34.7
|
1.0
|
O6
|
A:DG4
|
4.5
|
38.8
|
1.0
|
C5
|
A:DC3
|
4.5
|
35.7
|
1.0
|
O2
|
B:BRU8
|
4.5
|
42.7
|
1.0
|
C5
|
A:DG4
|
4.5
|
36.2
|
1.0
|
C8
|
A:DG4
|
4.6
|
43.1
|
1.0
|
N1
|
A:DG2
|
4.7
|
35.3
|
1.0
|
C6
|
A:DG4
|
4.8
|
39.6
|
1.0
|
C5
|
B:BRU8
|
4.9
|
38.4
|
1.0
|
C6
|
A:DC3
|
4.9
|
36.5
|
1.0
|
C6
|
B:DC9
|
5.0
|
39.0
|
1.0
|
|
Silver binding site 2 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 2 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 2 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag102
b:45.2
occ:1.00
|
N3
|
B:BRU8
|
1.9
|
34.1
|
1.0
|
N7
|
A:DG4
|
2.2
|
39.5
|
1.0
|
C2
|
B:BRU8
|
2.8
|
35.4
|
1.0
|
O2
|
B:BRU8
|
2.8
|
42.7
|
1.0
|
O6
|
A:DG4
|
2.9
|
38.8
|
1.0
|
AG
|
A:AG101
|
3.0
|
46.5
|
1.0
|
C5
|
A:DG4
|
3.0
|
36.2
|
1.0
|
C4
|
B:BRU8
|
3.1
|
37.9
|
1.0
|
AG
|
B:AG103
|
3.1
|
42.4
|
1.0
|
C6
|
A:DG4
|
3.3
|
39.6
|
1.0
|
O4
|
B:BRU8
|
3.3
|
38.5
|
1.0
|
C8
|
A:DG4
|
3.4
|
43.1
|
1.0
|
O2
|
A:DC5
|
3.5
|
35.8
|
1.0
|
O2
|
B:DC9
|
3.5
|
47.1
|
1.0
|
N3
|
A:DC3
|
3.6
|
36.5
|
1.0
|
N3
|
B:DC9
|
3.6
|
36.7
|
1.0
|
N3
|
A:DC5
|
3.7
|
36.2
|
1.0
|
C2
|
A:DC5
|
3.7
|
38.2
|
1.0
|
C2
|
B:DC9
|
3.7
|
42.7
|
1.0
|
N3
|
B:DC7
|
3.9
|
35.9
|
1.0
|
N4
|
A:DC3
|
4.1
|
43.0
|
1.0
|
C4
|
A:DC3
|
4.2
|
40.9
|
1.0
|
N1
|
B:BRU8
|
4.2
|
36.3
|
1.0
|
C2
|
A:DC3
|
4.3
|
38.9
|
1.0
|
C4
|
A:DG4
|
4.3
|
39.0
|
1.0
|
O
|
A:HOH202
|
4.3
|
34.1
|
1.0
|
C5
|
B:BRU8
|
4.4
|
38.4
|
1.0
|
O2
|
B:DC7
|
4.4
|
34.9
|
1.0
|
O2
|
A:DC3
|
4.4
|
39.7
|
1.0
|
N9
|
A:DG4
|
4.5
|
41.7
|
1.0
|
C4
|
B:DC9
|
4.5
|
35.8
|
1.0
|
C2
|
B:DC7
|
4.5
|
31.7
|
1.0
|
C4
|
A:DC5
|
4.6
|
35.3
|
1.0
|
N1
|
A:DC5
|
4.7
|
35.9
|
1.0
|
C4
|
B:DC7
|
4.7
|
40.8
|
1.0
|
N4
|
B:DC7
|
4.7
|
39.4
|
1.0
|
N1
|
A:DG4
|
4.7
|
37.1
|
1.0
|
N1
|
B:DC9
|
4.7
|
42.2
|
1.0
|
C6
|
B:BRU8
|
4.8
|
40.0
|
1.0
|
N4
|
B:DC9
|
4.9
|
35.8
|
1.0
|
|
Silver binding site 3 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 3 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 3 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag103
b:47.4
occ:1.00
|
N3
|
B:BRU6
|
1.9
|
36.5
|
1.0
|
N3
|
A:BRU6
|
1.9
|
36.9
|
1.0
|
C2
|
B:BRU6
|
2.8
|
37.6
|
1.0
|
C4
|
A:BRU6
|
2.9
|
37.9
|
1.0
|
O2
|
B:BRU6
|
2.9
|
37.5
|
1.0
|
C2
|
A:BRU6
|
3.0
|
40.1
|
1.0
|
C4
|
B:BRU6
|
3.0
|
40.4
|
1.0
|
AG
|
A:AG104
|
3.0
|
45.8
|
1.0
|
O4
|
A:BRU6
|
3.0
|
35.0
|
1.0
|
AG
|
B:AG103
|
3.1
|
42.4
|
1.0
|
O2
|
A:BRU6
|
3.1
|
42.0
|
1.0
|
O4
|
B:BRU6
|
3.2
|
44.1
|
1.0
|
N3
|
A:DC5
|
3.3
|
36.2
|
1.0
|
N3
|
B:DC5
|
3.4
|
39.5
|
1.0
|
N4
|
A:DC5
|
3.5
|
34.0
|
1.0
|
N4
|
B:DC5
|
3.6
|
42.5
|
1.0
|
C4
|
A:DC5
|
3.7
|
35.3
|
1.0
|
O2
|
B:DC7
|
3.7
|
34.9
|
1.0
|
C4
|
B:DC5
|
3.8
|
41.9
|
1.0
|
O
|
A:HOH201
|
3.8
|
37.8
|
1.0
|
N3
|
A:DC7
|
3.9
|
38.8
|
1.0
|
N3
|
B:DC7
|
3.9
|
35.9
|
1.0
|
O2
|
A:DC7
|
4.0
|
38.2
|
1.0
|
C2
|
B:DC7
|
4.0
|
31.7
|
1.0
|
C2
|
A:DC7
|
4.2
|
41.4
|
1.0
|
C2
|
A:DC5
|
4.2
|
38.2
|
1.0
|
N1
|
B:BRU6
|
4.3
|
39.8
|
1.0
|
C2
|
B:DC5
|
4.3
|
40.5
|
1.0
|
C5
|
A:BRU6
|
4.3
|
35.6
|
1.0
|
C5
|
B:BRU6
|
4.3
|
43.0
|
1.0
|
N1
|
A:BRU6
|
4.3
|
43.3
|
1.0
|
O2
|
A:DC5
|
4.5
|
35.8
|
1.0
|
O
|
B:HOH201
|
4.6
|
32.7
|
1.0
|
O2
|
B:DC5
|
4.6
|
40.8
|
1.0
|
C4
|
A:DC7
|
4.7
|
42.8
|
1.0
|
O
|
A:HOH202
|
4.8
|
34.1
|
1.0
|
C4
|
B:DC7
|
4.8
|
40.8
|
1.0
|
C6
|
B:BRU6
|
4.8
|
42.3
|
1.0
|
C6
|
A:BRU6
|
4.8
|
39.2
|
1.0
|
C5
|
A:DC5
|
4.9
|
38.2
|
1.0
|
C5
|
B:DC5
|
4.9
|
38.5
|
1.0
|
N4
|
A:DC7
|
5.0
|
41.2
|
1.0
|
N1
|
B:DC7
|
5.0
|
35.2
|
1.0
|
|
Silver binding site 4 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 4 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 4 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag104
b:45.8
occ:1.00
|
N3
|
B:DC5
|
2.0
|
39.5
|
1.0
|
N3
|
A:DC7
|
2.1
|
38.8
|
1.0
|
O6
|
B:DG4
|
2.7
|
46.0
|
1.0
|
C2
|
A:DC7
|
2.9
|
41.4
|
1.0
|
C2
|
B:DC5
|
2.9
|
40.5
|
1.0
|
O2
|
A:DC7
|
2.9
|
38.2
|
1.0
|
C4
|
B:DC5
|
3.0
|
41.9
|
1.0
|
C4
|
A:DC7
|
3.0
|
42.8
|
1.0
|
AG
|
A:AG103
|
3.0
|
47.4
|
1.0
|
O2
|
B:DC5
|
3.0
|
40.8
|
1.0
|
AG
|
A:AG105
|
3.1
|
51.9
|
1.0
|
N4
|
B:DC5
|
3.1
|
42.5
|
1.0
|
N4
|
A:DC7
|
3.2
|
41.2
|
1.0
|
O
|
B:HOH201
|
3.3
|
32.7
|
1.0
|
N3
|
A:BRU6
|
3.3
|
36.9
|
1.0
|
O4
|
A:BRU6
|
3.4
|
35.0
|
1.0
|
C6
|
B:DG4
|
3.4
|
41.1
|
1.0
|
C4
|
A:BRU6
|
3.6
|
37.9
|
1.0
|
N7
|
B:DG4
|
3.8
|
39.8
|
1.0
|
N3
|
B:BRU6
|
3.8
|
36.5
|
1.0
|
C5
|
B:DG4
|
3.8
|
41.0
|
1.0
|
N3
|
A:BRU8
|
3.8
|
38.6
|
1.0
|
O2
|
B:BRU6
|
3.9
|
37.5
|
1.0
|
C2
|
B:BRU6
|
4.1
|
37.6
|
1.0
|
N1
|
B:DC5
|
4.2
|
40.4
|
1.0
|
N1
|
A:DC7
|
4.2
|
43.2
|
1.0
|
C5
|
B:DC5
|
4.3
|
38.5
|
1.0
|
C2
|
A:BRU6
|
4.4
|
40.1
|
1.0
|
C2
|
A:BRU8
|
4.4
|
38.6
|
1.0
|
C5
|
A:DC7
|
4.4
|
41.4
|
1.0
|
O2
|
A:BRU8
|
4.4
|
39.9
|
1.0
|
N1
|
B:DG4
|
4.5
|
43.2
|
1.0
|
C4
|
A:BRU8
|
4.5
|
45.9
|
1.0
|
C4
|
B:BRU6
|
4.7
|
40.4
|
1.0
|
O2
|
A:BRU6
|
4.7
|
42.0
|
1.0
|
C5
|
A:BRU6
|
4.7
|
35.6
|
1.0
|
O4
|
A:BRU8
|
4.7
|
50.5
|
1.0
|
C6
|
B:DC5
|
4.8
|
39.2
|
1.0
|
C6
|
A:DC7
|
4.8
|
41.3
|
1.0
|
C8
|
B:DG4
|
4.9
|
42.2
|
1.0
|
|
Silver binding site 5 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 5 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 5 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag105
b:51.9
occ:1.00
|
N3
|
A:BRU8
|
1.9
|
38.6
|
1.0
|
N7
|
B:DG4
|
2.0
|
39.8
|
1.0
|
O2
|
A:BRU8
|
2.7
|
39.9
|
1.0
|
C2
|
A:BRU8
|
2.7
|
38.6
|
1.0
|
C5
|
B:DG4
|
2.9
|
41.0
|
1.0
|
O6
|
B:DG4
|
3.0
|
46.0
|
1.0
|
AG
|
A:AG104
|
3.1
|
45.8
|
1.0
|
AG
|
A:AG106
|
3.1
|
53.4
|
1.0
|
C8
|
B:DG4
|
3.1
|
42.2
|
1.0
|
C4
|
A:BRU8
|
3.1
|
45.9
|
1.0
|
O2
|
A:DC9
|
3.3
|
45.9
|
1.0
|
C6
|
B:DG4
|
3.3
|
41.1
|
1.0
|
O2
|
B:DC5
|
3.5
|
40.8
|
1.0
|
O4
|
A:BRU8
|
3.5
|
50.5
|
1.0
|
C2
|
A:DC9
|
3.6
|
42.4
|
1.0
|
N3
|
A:DC9
|
3.6
|
38.3
|
1.0
|
N3
|
B:DC5
|
3.7
|
39.5
|
1.0
|
C2
|
B:DC5
|
3.7
|
40.5
|
1.0
|
N3
|
A:DC7
|
3.7
|
38.8
|
1.0
|
N3
|
B:DC3
|
3.7
|
44.0
|
1.0
|
O
|
B:HOH201
|
3.9
|
32.7
|
1.0
|
C4
|
B:DG4
|
4.2
|
44.8
|
1.0
|
N1
|
A:BRU8
|
4.2
|
39.1
|
1.0
|
N9
|
B:DG4
|
4.2
|
43.5
|
1.0
|
N4
|
B:DC3
|
4.3
|
47.7
|
1.0
|
C2
|
A:DC7
|
4.3
|
41.4
|
1.0
|
C4
|
A:DC7
|
4.3
|
42.8
|
1.0
|
O2
|
A:DC7
|
4.4
|
38.2
|
1.0
|
N4
|
A:DC7
|
4.4
|
41.2
|
1.0
|
C4
|
B:DC3
|
4.4
|
43.4
|
1.0
|
C5
|
A:BRU8
|
4.4
|
44.6
|
1.0
|
C2
|
B:DC3
|
4.4
|
47.1
|
1.0
|
O2
|
B:DC3
|
4.5
|
47.6
|
1.0
|
C4
|
A:DC9
|
4.5
|
40.4
|
1.0
|
N1
|
A:DC9
|
4.6
|
44.1
|
1.0
|
C4
|
B:DC5
|
4.6
|
41.9
|
1.0
|
N1
|
B:DC5
|
4.7
|
40.4
|
1.0
|
N1
|
B:DG4
|
4.7
|
43.2
|
1.0
|
C6
|
A:BRU8
|
4.8
|
43.6
|
1.0
|
|
Silver binding site 6 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 6 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 6 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag106
b:53.4
occ:1.00
|
N3
|
A:DC9
|
2.0
|
38.3
|
1.0
|
N3
|
B:DC3
|
2.1
|
44.0
|
1.0
|
O2
|
B:DC3
|
2.8
|
47.6
|
1.0
|
C2
|
B:DC3
|
2.8
|
47.1
|
1.0
|
C2
|
A:DC9
|
2.8
|
42.4
|
1.0
|
O2
|
A:DC9
|
2.9
|
45.9
|
1.0
|
C4
|
A:DC9
|
3.0
|
40.4
|
1.0
|
O6
|
B:DG2
|
3.0
|
52.2
|
1.0
|
AG
|
A:AG105
|
3.1
|
51.9
|
1.0
|
C4
|
B:DC3
|
3.1
|
43.4
|
1.0
|
AG
|
A:AG107
|
3.2
|
51.6
|
1.0
|
N4
|
A:DC9
|
3.2
|
49.0
|
1.0
|
N3
|
A:BRU8
|
3.3
|
38.6
|
1.0
|
O4
|
A:BRU8
|
3.4
|
50.5
|
1.0
|
N4
|
B:DC3
|
3.4
|
47.7
|
1.0
|
C4
|
A:BRU8
|
3.6
|
45.9
|
1.0
|
C6
|
B:DG2
|
3.7
|
49.5
|
1.0
|
N7
|
B:DG4
|
3.8
|
39.8
|
1.0
|
N7
|
B:DG2
|
3.8
|
44.6
|
1.0
|
O6
|
A:DG10
|
4.0
|
45.6
|
1.0
|
N7
|
A:DG10
|
4.0
|
39.7
|
1.0
|
C5
|
B:DG2
|
4.0
|
46.3
|
1.0
|
N1
|
B:DC3
|
4.2
|
47.4
|
1.0
|
N1
|
A:DC9
|
4.2
|
44.1
|
1.0
|
C5
|
A:DG10
|
4.3
|
40.6
|
1.0
|
C6
|
A:DG10
|
4.3
|
41.4
|
1.0
|
C5
|
B:DG4
|
4.3
|
41.0
|
1.0
|
C5
|
A:DC9
|
4.3
|
43.0
|
1.0
|
C2
|
A:BRU8
|
4.3
|
38.6
|
1.0
|
C8
|
B:DG4
|
4.4
|
42.2
|
1.0
|
C5
|
B:DC3
|
4.4
|
47.4
|
1.0
|
O6
|
B:DG4
|
4.5
|
46.0
|
1.0
|
C6
|
B:DG4
|
4.6
|
41.1
|
1.0
|
O2
|
A:BRU8
|
4.7
|
39.9
|
1.0
|
C6
|
A:DC9
|
4.8
|
47.3
|
1.0
|
C5
|
A:BRU8
|
4.8
|
44.6
|
1.0
|
C6
|
B:DC3
|
4.8
|
48.6
|
1.0
|
C8
|
A:DG10
|
4.8
|
44.3
|
1.0
|
N1
|
B:DG2
|
4.8
|
48.9
|
1.0
|
C8
|
B:DG2
|
4.9
|
46.4
|
1.0
|
|
Silver binding site 7 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 7 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 7 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag107
b:51.6
occ:1.00
|
N7
|
A:DG10
|
2.1
|
39.7
|
1.0
|
N7
|
B:DG2
|
2.2
|
44.6
|
1.0
|
O2
|
B:DC3
|
2.9
|
47.6
|
1.0
|
C5
|
A:DG10
|
3.0
|
40.6
|
1.0
|
O2
|
A:DC11
|
3.0
|
46.7
|
1.0
|
AG
|
A:AG108
|
3.0
|
52.1
|
1.0
|
O6
|
A:DG10
|
3.0
|
45.6
|
1.0
|
C8
|
B:DG2
|
3.0
|
46.4
|
1.0
|
C8
|
A:DG10
|
3.2
|
44.3
|
1.0
|
AG
|
A:AG106
|
3.2
|
53.4
|
1.0
|
C2
|
A:DC11
|
3.2
|
42.6
|
1.0
|
C2
|
B:DC3
|
3.3
|
47.1
|
1.0
|
C5
|
B:DG2
|
3.3
|
46.3
|
1.0
|
C6
|
A:DG10
|
3.3
|
41.4
|
1.0
|
N3
|
A:DC11
|
3.3
|
37.6
|
1.0
|
N3
|
B:DC3
|
3.6
|
44.0
|
1.0
|
O6
|
B:DG2
|
3.7
|
52.2
|
1.0
|
C6
|
B:DG2
|
3.9
|
49.5
|
1.0
|
N3
|
A:DC9
|
4.0
|
38.3
|
1.0
|
N1
|
B:DC3
|
4.1
|
47.4
|
1.0
|
N3
|
B:DC1
|
4.1
|
47.5
|
1.0
|
N1
|
A:DC11
|
4.2
|
48.2
|
1.0
|
C4
|
A:DG10
|
4.2
|
44.1
|
1.0
|
C4
|
A:DC11
|
4.3
|
39.1
|
1.0
|
N9
|
B:DG2
|
4.3
|
49.4
|
1.0
|
N9
|
A:DG10
|
4.3
|
46.3
|
1.0
|
C4
|
B:DG2
|
4.4
|
47.7
|
1.0
|
C1'
|
B:DC3
|
4.5
|
50.6
|
1.0
|
C4
|
B:DC3
|
4.6
|
43.4
|
1.0
|
O2
|
A:DC9
|
4.6
|
45.9
|
1.0
|
C2
|
A:DC9
|
4.6
|
42.4
|
1.0
|
N4
|
A:DC9
|
4.7
|
49.0
|
1.0
|
C4
|
A:DC9
|
4.7
|
40.4
|
1.0
|
N4
|
B:DC1
|
4.7
|
45.9
|
1.0
|
N1
|
A:DG10
|
4.7
|
41.4
|
1.0
|
O2
|
B:DC1
|
4.8
|
49.4
|
1.0
|
C1'
|
A:DC11
|
4.8
|
48.6
|
1.0
|
C2
|
B:DC1
|
4.9
|
48.9
|
1.0
|
C4
|
B:DC1
|
4.9
|
46.5
|
1.0
|
N4
|
A:DC11
|
4.9
|
42.0
|
1.0
|
C6
|
A:DC11
|
5.0
|
46.0
|
1.0
|
C6
|
B:DC3
|
5.0
|
48.6
|
1.0
|
|
Silver binding site 8 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 8 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 8 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag108
b:52.1
occ:1.00
|
N3
|
A:DC11
|
2.1
|
37.6
|
1.0
|
N3
|
B:DC1
|
2.1
|
47.5
|
1.0
|
O6
|
A:DG10
|
2.8
|
45.6
|
1.0
|
C4
|
A:DC11
|
2.9
|
39.1
|
1.0
|
N4
|
A:DC11
|
3.0
|
42.0
|
1.0
|
C2
|
B:DC1
|
3.0
|
48.9
|
1.0
|
AG
|
A:AG107
|
3.0
|
51.6
|
1.0
|
C4
|
B:DC1
|
3.0
|
46.5
|
1.0
|
C2
|
A:DC11
|
3.0
|
42.6
|
1.0
|
O2
|
B:DC1
|
3.1
|
49.4
|
1.0
|
N4
|
B:DC1
|
3.1
|
45.9
|
1.0
|
O2
|
A:DC11
|
3.2
|
46.7
|
1.0
|
O6
|
C:DG12
|
3.2
|
48.8
|
1.0
|
O6
|
A:DG12
|
3.3
|
43.6
|
1.0
|
N7
|
B:DG2
|
3.5
|
44.6
|
1.0
|
C6
|
A:DG10
|
3.5
|
41.4
|
1.0
|
C6
|
C:DG12
|
3.5
|
48.2
|
1.0
|
N1
|
A:DG12
|
3.6
|
47.8
|
1.0
|
N1
|
C:DG12
|
3.6
|
46.1
|
1.0
|
C6
|
A:DG12
|
3.7
|
44.9
|
1.0
|
N7
|
A:DG10
|
3.9
|
39.7
|
1.0
|
C5
|
A:DG10
|
3.9
|
40.6
|
1.0
|
C5
|
B:DG2
|
4.1
|
46.3
|
1.0
|
C8
|
B:DG2
|
4.1
|
46.4
|
1.0
|
C5
|
A:DC11
|
4.3
|
38.4
|
1.0
|
O6
|
B:DG2
|
4.3
|
52.2
|
1.0
|
N1
|
B:DC1
|
4.3
|
47.6
|
1.0
|
N1
|
A:DC11
|
4.3
|
48.2
|
1.0
|
C5
|
B:DC1
|
4.4
|
48.8
|
1.0
|
C5
|
C:DG12
|
4.4
|
47.2
|
1.0
|
C6
|
B:DG2
|
4.4
|
49.5
|
1.0
|
N1
|
A:DG10
|
4.6
|
41.4
|
1.0
|
C2
|
C:DG12
|
4.6
|
50.2
|
1.0
|
C2
|
A:DG12
|
4.6
|
53.4
|
1.0
|
C6
|
A:DC11
|
4.8
|
46.0
|
1.0
|
C5
|
A:DG12
|
4.8
|
43.2
|
1.0
|
C6
|
B:DC1
|
4.8
|
50.7
|
1.0
|
N2
|
A:DG12
|
5.0
|
52.0
|
1.0
|
C8
|
A:DG10
|
5.0
|
44.3
|
1.0
|
C4
|
B:DG2
|
5.0
|
47.7
|
1.0
|
|
Silver binding site 9 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 9 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 9 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag109
b:98.2
occ:1.00
|
C4'
|
A:DC9
|
4.1
|
47.9
|
1.0
|
C5'
|
B:BRU6
|
4.2
|
42.7
|
1.0
|
C5'
|
A:DC9
|
4.6
|
48.8
|
1.0
|
O3'
|
A:DC9
|
4.7
|
54.7
|
1.0
|
O4'
|
A:DC9
|
4.9
|
48.5
|
1.0
|
|
Silver binding site 10 out
of 23 in 7xkm
Go back to
Silver Binding Sites List in 7xkm
Silver binding site 10 out
of 23 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 10 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag101
b:43.8
occ:1.00
|
N3
|
B:DC11
|
2.2
|
41.5
|
1.0
|
N3
|
A:DC1
|
2.2
|
40.9
|
1.0
|
O2
|
A:DC1
|
2.8
|
42.8
|
1.0
|
C2
|
A:DC1
|
2.9
|
40.2
|
1.0
|
AG
|
B:AG102
|
3.0
|
49.2
|
1.0
|
O6
|
B:DG10
|
3.0
|
45.1
|
1.0
|
C4
|
B:DC11
|
3.1
|
42.6
|
1.0
|
C2
|
B:DC11
|
3.1
|
42.8
|
1.0
|
N4
|
B:DC11
|
3.2
|
41.0
|
1.0
|
O2
|
B:DC11
|
3.2
|
41.6
|
1.0
|
C4
|
A:DC1
|
3.3
|
38.3
|
1.0
|
N7
|
A:DG2
|
3.6
|
39.9
|
1.0
|
N4
|
A:DC1
|
3.6
|
38.3
|
1.0
|
C6
|
B:DG10
|
3.6
|
42.4
|
1.0
|
O6
|
A:DG2
|
3.7
|
43.6
|
1.0
|
N7
|
B:DG10
|
3.8
|
38.9
|
1.0
|
N1
|
B:DG12
|
3.9
|
38.4
|
1.0
|
C5
|
A:DG2
|
3.9
|
37.5
|
1.0
|
N2
|
B:DG12
|
4.0
|
45.2
|
1.0
|
C5
|
B:DG10
|
4.0
|
41.0
|
1.0
|
C6
|
A:DG2
|
4.0
|
39.8
|
1.0
|
N1
|
A:DC1
|
4.2
|
38.4
|
1.0
|
C2
|
B:DG12
|
4.4
|
42.8
|
1.0
|
C8
|
A:DG2
|
4.4
|
42.1
|
1.0
|
N1
|
B:DC11
|
4.4
|
46.7
|
1.0
|
C5
|
B:DC11
|
4.5
|
41.2
|
1.0
|
C5
|
A:DC1
|
4.6
|
35.4
|
1.0
|
N1
|
B:DG10
|
4.7
|
38.8
|
1.0
|
C6
|
B:DG12
|
4.8
|
45.1
|
1.0
|
C6
|
A:DC1
|
4.9
|
37.7
|
1.0
|
C8
|
B:DG10
|
4.9
|
39.0
|
1.0
|
O6
|
B:DG12
|
5.0
|
48.6
|
1.0
|
C6
|
B:DC11
|
5.0
|
42.6
|
1.0
|
C4
|
A:DG2
|
5.0
|
38.6
|
1.0
|
|
Reference:
T.Atsugi,
A.Ono,
M.Tasaka,
N.Eguchi,
S.Fujiwara,
J.Kondo.
A Novel Ag I -Dna Rod Comprising A One-Dimensional Array of 11 Silver Ions Within A Double Helical Structure. Angew.Chem.Int.Ed.Engl. V. 61 04798 2022.
ISSN: ESSN 1521-3773
PubMed: 35641885
DOI: 10.1002/ANIE.202204798
Page generated: Wed Jul 10 09:03:06 2024
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