Silver in PDB 8dyk: Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Silver Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Silver atom in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
(pdb code 8dyk). This binding sites where shown within
5.0 Angstroms radius around Silver atom.
In total 11 binding sites of Silver where determined in the
Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold, PDB code: 8dyk:
Jump to Silver binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Silver binding site 1 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 1 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 1 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag101
b:20.1
occ:1.00
|
N3
|
B:DC5
|
2.2
|
13.1
|
1.0
|
N3
|
A:DC5
|
2.2
|
15.0
|
1.0
|
D42
|
A:DC5
|
2.6
|
20.2
|
1.0
|
O2
|
B:DC5
|
2.8
|
22.2
|
1.0
|
C2
|
B:DC5
|
2.9
|
16.3
|
1.0
|
D42
|
B:DC5
|
2.9
|
20.5
|
1.0
|
O2
|
B:DC6
|
3.0
|
16.9
|
1.0
|
AG
|
A:AG108
|
3.1
|
10.8
|
1.0
|
C2
|
A:DC5
|
3.1
|
25.1
|
1.0
|
N3
|
A:DC6
|
3.1
|
10.4
|
1.0
|
D42
|
B:DC4
|
3.1
|
19.9
|
1.0
|
O2
|
A:DC6
|
3.1
|
7.6
|
1.0
|
C4
|
A:DC5
|
3.1
|
11.9
|
1.0
|
O2
|
A:DC5
|
3.2
|
12.2
|
1.0
|
C4
|
B:DC5
|
3.2
|
9.9
|
1.0
|
N4
|
A:DC5
|
3.2
|
17.3
|
1.0
|
C2
|
A:DC6
|
3.4
|
6.1
|
1.0
|
N4
|
B:DC5
|
3.4
|
17.5
|
1.0
|
C2
|
B:DC6
|
3.5
|
8.4
|
1.0
|
N4
|
B:DC4
|
3.5
|
17.0
|
1.0
|
N3
|
B:DC6
|
3.6
|
25.8
|
1.0
|
AG
|
A:AG102
|
3.6
|
10.1
|
1.0
|
D42
|
A:DC4
|
3.8
|
23.9
|
1.0
|
N3
|
B:DC4
|
3.9
|
6.2
|
1.0
|
C4
|
B:DC4
|
3.9
|
19.4
|
1.0
|
D41
|
B:DC4
|
4.0
|
19.9
|
1.0
|
C4
|
A:DC6
|
4.1
|
17.3
|
1.0
|
D42
|
A:DC6
|
4.1
|
33.0
|
1.0
|
D41
|
A:DC5
|
4.2
|
20.2
|
1.0
|
N1
|
B:DC5
|
4.2
|
15.3
|
1.0
|
N3
|
A:DC4
|
4.3
|
16.4
|
1.0
|
N4
|
A:DC4
|
4.4
|
20.3
|
1.0
|
N1
|
A:DC5
|
4.4
|
16.4
|
1.0
|
D41
|
B:DC5
|
4.5
|
20.5
|
1.0
|
N4
|
A:DC6
|
4.5
|
27.9
|
1.0
|
H1'
|
B:DC6
|
4.5
|
24.1
|
1.0
|
C5
|
A:DC5
|
4.5
|
19.1
|
1.0
|
C5
|
B:DC5
|
4.5
|
8.4
|
1.0
|
N1
|
A:DC6
|
4.5
|
7.9
|
1.0
|
N1
|
B:DC6
|
4.5
|
20.1
|
1.0
|
C4
|
B:DC6
|
4.7
|
20.8
|
1.0
|
C4
|
A:DC4
|
4.7
|
23.1
|
1.0
|
C2
|
B:DC4
|
4.9
|
10.3
|
1.0
|
C6
|
B:DC5
|
4.9
|
10.8
|
1.0
|
C6
|
A:DC5
|
5.0
|
10.3
|
1.0
|
C5
|
B:DC4
|
5.0
|
16.6
|
1.0
|
D42
|
B:DC6
|
5.0
|
18.3
|
1.0
|
|
Silver binding site 2 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 2 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 2 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag102
b:10.1
occ:1.00
|
N3
|
A:DC4
|
2.2
|
16.4
|
1.0
|
N3
|
B:DC4
|
2.2
|
6.2
|
1.0
|
O2
|
B:DC4
|
2.6
|
18.0
|
1.0
|
D42
|
A:DC4
|
2.7
|
23.9
|
1.0
|
C2
|
B:DC4
|
2.8
|
10.3
|
1.0
|
O2
|
B:DC5
|
3.0
|
22.2
|
1.0
|
C2
|
A:DC4
|
3.0
|
18.6
|
1.0
|
O2
|
A:DC4
|
3.1
|
14.5
|
1.0
|
C4
|
A:DC4
|
3.1
|
23.1
|
1.0
|
AG
|
B:AG101
|
3.1
|
2.4
|
1.0
|
D1
|
A:HOH202
|
3.2
|
21.0
|
1.0
|
O
|
A:HOH202
|
3.2
|
17.9
|
1.0
|
D42
|
B:DC4
|
3.2
|
19.9
|
1.0
|
N4
|
A:DC4
|
3.2
|
20.3
|
1.0
|
D41
|
A:DC3
|
3.2
|
17.8
|
1.0
|
D42
|
B:DC3
|
3.3
|
21.4
|
1.0
|
C4
|
B:DC4
|
3.3
|
19.4
|
1.0
|
N4
|
A:DC3
|
3.5
|
15.2
|
1.0
|
C2
|
B:DC5
|
3.5
|
16.3
|
1.0
|
AG
|
A:AG101
|
3.6
|
20.1
|
1.0
|
N4
|
B:DC4
|
3.7
|
17.0
|
1.0
|
D2
|
A:HOH202
|
3.7
|
21.0
|
1.0
|
N3
|
B:DC5
|
3.8
|
13.1
|
1.0
|
N3
|
B:DC3
|
3.9
|
20.3
|
1.0
|
N4
|
B:DC3
|
3.9
|
18.3
|
1.0
|
N3
|
A:DC5
|
4.0
|
15.0
|
1.0
|
N1
|
B:DC4
|
4.2
|
15.9
|
1.0
|
C4
|
A:DC3
|
4.2
|
11.7
|
1.0
|
O2
|
A:DC5
|
4.2
|
12.2
|
1.0
|
D41
|
A:DC4
|
4.2
|
23.9
|
1.0
|
C4
|
B:DC3
|
4.3
|
16.4
|
1.0
|
N1
|
A:DC4
|
4.3
|
12.5
|
1.0
|
C2
|
A:DC5
|
4.3
|
25.1
|
1.0
|
D1
|
B:HOH205
|
4.4
|
37.5
|
1.0
|
N1
|
B:DC5
|
4.4
|
15.3
|
1.0
|
C5
|
A:DC4
|
4.4
|
14.5
|
1.0
|
H1'
|
B:DC5
|
4.5
|
10.1
|
1.0
|
C5
|
B:DC4
|
4.6
|
16.6
|
1.0
|
D41
|
B:DC3
|
4.6
|
21.4
|
1.0
|
D42
|
A:DC5
|
4.7
|
20.2
|
1.0
|
D41
|
B:DC4
|
4.7
|
19.9
|
1.0
|
H5
|
A:DC3
|
4.7
|
8.7
|
1.0
|
C5
|
A:DC3
|
4.8
|
7.6
|
1.0
|
C2
|
B:DC3
|
4.8
|
21.9
|
1.0
|
C4
|
A:DC5
|
4.8
|
11.9
|
1.0
|
N3
|
A:DC3
|
4.8
|
8.1
|
1.0
|
O4'
|
B:DC5
|
4.8
|
28.1
|
1.0
|
C1'
|
B:DC5
|
4.9
|
8.8
|
1.0
|
C4
|
B:DC5
|
4.9
|
9.9
|
1.0
|
H1'
|
B:DC4
|
4.9
|
22.8
|
1.0
|
C6
|
B:DC4
|
4.9
|
9.4
|
1.0
|
C6
|
A:DC4
|
4.9
|
7.0
|
1.0
|
O2
|
B:DC3
|
5.0
|
27.7
|
1.0
|
|
Silver binding site 3 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 3 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 3 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag103
b:7.7
occ:1.00
|
N6
|
B:DA2
|
2.1
|
12.7
|
1.0
|
N3
|
A:DC3
|
2.3
|
8.1
|
1.0
|
D62
|
B:DA2
|
2.4
|
14.7
|
0.2
|
H62
|
B:DA2
|
2.4
|
14.7
|
0.8
|
D2
|
A:HOH206
|
2.5
|
5.7
|
0.5
|
D1
|
A:HOH206
|
2.7
|
5.7
|
0.5
|
O2
|
A:DC3
|
2.7
|
10.9
|
1.0
|
AG
|
B:AG101
|
2.8
|
2.4
|
1.0
|
C2
|
A:DC3
|
2.9
|
8.8
|
1.0
|
H2
|
B:DA1
|
2.9
|
18.4
|
1.0
|
AG
|
B:AG102
|
3.0
|
14.2
|
1.0
|
O
|
A:HOH206
|
3.1
|
5.2
|
0.5
|
H1'
|
A:DC4
|
3.2
|
8.6
|
1.0
|
C6
|
B:DA2
|
3.2
|
16.5
|
1.0
|
C4
|
A:DC3
|
3.4
|
11.7
|
1.0
|
O2
|
A:DC4
|
3.5
|
14.5
|
1.0
|
C2
|
B:DA1
|
3.6
|
15.8
|
1.0
|
N1
|
B:DA2
|
3.7
|
14.2
|
1.0
|
N4
|
A:DC3
|
3.7
|
15.2
|
1.0
|
D42
|
B:DC3
|
3.8
|
21.4
|
1.0
|
AG
|
A:AG106
|
3.8
|
12.4
|
1.0
|
N1
|
A:DA2
|
3.9
|
2.4
|
1.0
|
N6
|
A:DA2
|
4.0
|
10.8
|
1.0
|
C6
|
A:DA2
|
4.1
|
8.2
|
1.0
|
N3
|
B:DA1
|
4.1
|
17.4
|
1.0
|
C1'
|
A:DC4
|
4.2
|
7.6
|
1.0
|
C2
|
A:DC4
|
4.2
|
18.6
|
1.0
|
N3
|
B:DC3
|
4.2
|
20.3
|
1.0
|
N1
|
A:DC3
|
4.2
|
11.6
|
1.0
|
N1
|
B:DA1
|
4.4
|
18.1
|
1.0
|
N4
|
B:DC3
|
4.4
|
18.3
|
1.0
|
C5
|
B:DA2
|
4.5
|
7.8
|
1.0
|
N1
|
A:DC4
|
4.5
|
12.5
|
1.0
|
C2
|
A:DA2
|
4.6
|
14.1
|
1.0
|
O4'
|
A:DC4
|
4.6
|
5.6
|
1.0
|
C4
|
B:DC3
|
4.7
|
16.4
|
1.0
|
C5
|
A:DC3
|
4.7
|
7.6
|
1.0
|
D41
|
A:DC3
|
4.7
|
17.8
|
1.0
|
D61
|
A:DA2
|
4.8
|
12.5
|
1.0
|
C5
|
A:DA2
|
4.9
|
7.9
|
1.0
|
H2
|
A:DA2
|
4.9
|
16.4
|
1.0
|
H1'
|
A:DC3
|
4.9
|
20.4
|
1.0
|
C6
|
A:DC3
|
5.0
|
9.1
|
1.0
|
|
Silver binding site 4 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 4 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 4 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag104
b:2.4
occ:1.00
|
O
|
A:HOH213
|
2.2
|
23.1
|
1.0
|
N7
|
A:DA2
|
2.4
|
12.3
|
1.0
|
D41
|
A:DC3
|
2.7
|
17.8
|
1.0
|
O
|
A:HOH202
|
2.9
|
17.9
|
1.0
|
D1
|
A:HOH202
|
2.9
|
21.0
|
1.0
|
O
|
B:HOH205
|
3.0
|
31.6
|
1.0
|
O
|
A:HOH212
|
3.1
|
8.9
|
1.0
|
D1
|
B:HOH205
|
3.1
|
37.5
|
1.0
|
H8
|
A:DA2
|
3.2
|
16.1
|
1.0
|
C8
|
A:DA2
|
3.2
|
13.8
|
1.0
|
D61
|
A:DA2
|
3.2
|
12.5
|
1.0
|
D2
|
A:HOH202
|
3.3
|
21.0
|
1.0
|
N4
|
A:DC3
|
3.3
|
15.2
|
1.0
|
H5
|
A:DC3
|
3.6
|
8.7
|
1.0
|
C5
|
A:DA2
|
3.6
|
7.9
|
1.0
|
H2'
|
A:DA1
|
3.7
|
14.2
|
1.0
|
D2
|
B:HOH205
|
3.9
|
37.5
|
1.0
|
N7
|
A:DA1
|
4.0
|
18.5
|
1.0
|
N6
|
A:DA2
|
4.0
|
10.8
|
1.0
|
C8
|
A:DA1
|
4.0
|
13.8
|
1.0
|
C4
|
A:DC3
|
4.0
|
11.7
|
1.0
|
H4'
|
B:DC5
|
4.0
|
17.7
|
1.0
|
C5
|
A:DC3
|
4.1
|
7.6
|
1.0
|
H3'
|
A:DA1
|
4.1
|
22.6
|
1.0
|
H8
|
A:DA1
|
4.2
|
16.1
|
1.0
|
C6
|
A:DA2
|
4.2
|
8.2
|
1.0
|
H5'
|
B:DC5
|
4.3
|
31.7
|
1.0
|
OP2
|
A:DA2
|
4.3
|
19.0
|
1.0
|
O2
|
B:DC4
|
4.3
|
18.0
|
1.0
|
C5
|
A:DA1
|
4.4
|
2.4
|
1.0
|
O
|
A:HOH203
|
4.4
|
11.4
|
1.0
|
N9
|
A:DA1
|
4.4
|
9.3
|
1.0
|
N9
|
A:DA2
|
4.5
|
16.6
|
1.0
|
C2'
|
A:DA1
|
4.6
|
12.2
|
1.0
|
H1'
|
B:DC4
|
4.6
|
22.8
|
1.0
|
C4
|
A:DA1
|
4.7
|
11.2
|
1.0
|
C4
|
A:DA2
|
4.7
|
7.8
|
1.0
|
C4'
|
B:DC5
|
4.8
|
15.1
|
1.0
|
C3'
|
A:DA1
|
4.9
|
19.3
|
1.0
|
O4'
|
B:DC5
|
4.9
|
28.1
|
1.0
|
C5'
|
B:DC5
|
5.0
|
26.8
|
1.0
|
|
Silver binding site 5 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 5 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 5 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag105
b:6.5
occ:1.00
|
D61
|
A:DA1
|
2.0
|
22.6
|
1.0
|
N1
|
A:DA1
|
2.2
|
17.2
|
1.0
|
D2
|
A:HOH205
|
2.4
|
32.3
|
0.7
|
O
|
A:HOH205
|
2.5
|
27.3
|
0.7
|
N6
|
A:DA1
|
2.7
|
19.2
|
1.0
|
C6
|
A:DA1
|
2.9
|
15.2
|
1.0
|
C2
|
A:DA1
|
3.3
|
17.9
|
1.0
|
D1
|
A:HOH205
|
3.4
|
32.3
|
0.7
|
H2
|
B:DA2
|
3.4
|
13.7
|
1.0
|
AG
|
B:AG102
|
3.4
|
14.2
|
1.0
|
H2
|
A:DA1
|
3.5
|
21.0
|
1.0
|
AG
|
A:AG106
|
3.7
|
12.4
|
1.0
|
D62
|
A:DA1
|
3.7
|
22.6
|
1.0
|
N6
|
A:DA2
|
3.8
|
10.8
|
1.0
|
D61
|
A:DA2
|
4.1
|
12.5
|
1.0
|
C2
|
B:DA2
|
4.1
|
11.8
|
1.0
|
N1
|
B:DA2
|
4.2
|
14.2
|
1.0
|
C5
|
A:DA1
|
4.2
|
2.4
|
1.0
|
N1
|
A:DA2
|
4.3
|
2.4
|
1.0
|
C6
|
A:DA2
|
4.4
|
8.2
|
1.0
|
N3
|
A:DA1
|
4.6
|
17.1
|
1.0
|
C4
|
A:DA1
|
4.8
|
11.2
|
1.0
|
D1
|
B:HOH207
|
5.0
|
44.3
|
1.0
|
|
Silver binding site 6 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 6 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 6 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag106
b:12.4
occ:1.00
|
N1
|
A:DA2
|
2.4
|
2.4
|
1.0
|
H2
|
A:DA2
|
2.9
|
16.4
|
1.0
|
D2
|
A:HOH206
|
2.9
|
5.7
|
0.5
|
O
|
A:HOH206
|
3.0
|
5.2
|
0.5
|
AG
|
B:AG102
|
3.0
|
14.2
|
1.0
|
C2
|
A:DA2
|
3.1
|
14.1
|
1.0
|
D1
|
A:HOH206
|
3.3
|
5.7
|
0.5
|
C6
|
A:DA2
|
3.4
|
8.2
|
1.0
|
N6
|
A:DA2
|
3.6
|
10.8
|
1.0
|
AG
|
A:AG105
|
3.7
|
6.5
|
1.0
|
AG
|
A:AG103
|
3.8
|
7.7
|
1.0
|
N1
|
B:DA2
|
4.1
|
14.2
|
1.0
|
N6
|
B:DA2
|
4.2
|
12.7
|
1.0
|
H2
|
A:DA1
|
4.2
|
21.0
|
1.0
|
N1
|
A:DA1
|
4.3
|
17.2
|
1.0
|
H2
|
B:DA1
|
4.4
|
18.4
|
1.0
|
C6
|
B:DA2
|
4.4
|
16.5
|
1.0
|
N3
|
A:DA2
|
4.4
|
6.7
|
1.0
|
D61
|
A:DA2
|
4.6
|
12.5
|
1.0
|
C2
|
A:DA1
|
4.6
|
17.9
|
1.0
|
C5
|
A:DA2
|
4.7
|
7.9
|
1.0
|
O2
|
A:DC3
|
4.7
|
10.9
|
1.0
|
D62
|
B:DA2
|
4.7
|
14.7
|
0.2
|
H62
|
B:DA2
|
4.7
|
14.7
|
0.8
|
N3
|
A:DC3
|
4.9
|
8.1
|
1.0
|
C2
|
B:DA2
|
4.9
|
11.8
|
1.0
|
C4
|
A:DA2
|
5.0
|
7.8
|
1.0
|
|
Silver binding site 7 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 7 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 7 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag107
b:12.8
occ:0.38
|
O
|
A:HOH215
|
2.3
|
11.3
|
0.4
|
N3
|
A:DA2
|
2.5
|
6.7
|
1.0
|
H1'
|
A:DA2
|
2.6
|
15.3
|
1.0
|
H5'
|
A:DC3
|
2.8
|
10.6
|
1.0
|
D1
|
A:HOH215
|
2.9
|
13.1
|
0.4
|
D2
|
A:HOH215
|
3.1
|
13.1
|
0.4
|
H2
|
A:DA2
|
3.1
|
16.4
|
1.0
|
C2
|
A:DA2
|
3.3
|
14.1
|
1.0
|
O4'
|
A:DC3
|
3.4
|
7.1
|
1.0
|
C4
|
A:DA2
|
3.6
|
7.8
|
1.0
|
C1'
|
A:DA2
|
3.6
|
13.2
|
1.0
|
C5'
|
A:DC3
|
3.7
|
9.2
|
1.0
|
H4'
|
A:DC3
|
3.8
|
12.8
|
1.0
|
C4'
|
A:DC3
|
3.9
|
11.1
|
1.0
|
N9
|
A:DA2
|
4.0
|
16.6
|
1.0
|
H5''
|
A:DC3
|
4.1
|
10.6
|
1.0
|
O4'
|
A:DA2
|
4.2
|
17.2
|
1.0
|
H2''
|
A:DA2
|
4.6
|
18.6
|
1.0
|
N1
|
A:DA2
|
4.6
|
2.4
|
1.0
|
C1'
|
A:DC3
|
4.7
|
17.4
|
1.0
|
O
|
A:HOH209
|
4.7
|
33.6
|
1.0
|
C2'
|
A:DA2
|
4.7
|
15.9
|
1.0
|
D1
|
A:HOH209
|
4.7
|
39.9
|
1.0
|
O3'
|
A:DA2
|
4.8
|
15.7
|
1.0
|
O5'
|
A:DC3
|
4.9
|
14.0
|
1.0
|
C5
|
A:DA2
|
4.9
|
7.9
|
1.0
|
|
Silver binding site 8 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 8 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 8 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag108
b:10.8
occ:1.00
|
N3
|
B:DC6
|
2.2
|
25.8
|
1.0
|
N3
|
A:DC6
|
2.3
|
10.4
|
1.0
|
D42
|
A:DC6
|
2.7
|
33.0
|
1.0
|
D42
|
B:DC6
|
2.8
|
18.3
|
1.0
|
C2
|
B:DC6
|
3.0
|
8.4
|
1.0
|
O2
|
B:DC6
|
3.0
|
16.9
|
1.0
|
AG
|
A:AG101
|
3.1
|
20.1
|
1.0
|
C2
|
A:DC6
|
3.1
|
6.1
|
1.0
|
D42
|
B:DC5
|
3.2
|
20.5
|
1.0
|
C4
|
A:DC6
|
3.2
|
17.3
|
1.0
|
C4
|
B:DC6
|
3.2
|
20.8
|
1.0
|
O2
|
A:DC6
|
3.2
|
7.6
|
1.0
|
N4
|
A:DC6
|
3.3
|
27.9
|
1.0
|
N4
|
B:DC6
|
3.4
|
15.6
|
1.0
|
N4
|
B:DC5
|
3.7
|
17.5
|
1.0
|
N3
|
B:DC5
|
3.7
|
13.1
|
1.0
|
D42
|
A:DC5
|
3.9
|
20.2
|
1.0
|
C4
|
B:DC5
|
4.0
|
9.9
|
1.0
|
D41
|
A:DC6
|
4.3
|
33.0
|
1.0
|
D41
|
B:DC5
|
4.3
|
20.5
|
1.0
|
N3
|
A:DC5
|
4.3
|
15.0
|
1.0
|
N1
|
B:DC6
|
4.3
|
20.1
|
1.0
|
D41
|
B:DC6
|
4.4
|
18.3
|
1.0
|
N1
|
A:DC6
|
4.4
|
7.9
|
1.0
|
N4
|
A:DC5
|
4.5
|
17.3
|
1.0
|
C5
|
A:DC6
|
4.5
|
7.3
|
1.0
|
C5
|
B:DC6
|
4.5
|
7.9
|
1.0
|
C2
|
B:DC5
|
4.6
|
16.3
|
1.0
|
C4
|
A:DC5
|
4.8
|
11.9
|
1.0
|
C6
|
B:DC6
|
4.9
|
21.7
|
1.0
|
C6
|
A:DC6
|
5.0
|
22.2
|
1.0
|
O2
|
B:DC5
|
5.0
|
22.2
|
1.0
|
|
Silver binding site 9 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 9 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 9 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag101
b:2.4
occ:1.00
|
N3
|
B:DC3
|
2.2
|
20.3
|
1.0
|
N4
|
A:DC3
|
2.2
|
15.2
|
1.0
|
D42
|
B:DC3
|
2.6
|
21.4
|
1.0
|
AG
|
A:AG103
|
2.8
|
7.7
|
1.0
|
D41
|
A:DC3
|
2.9
|
17.8
|
1.0
|
C4
|
A:DC3
|
3.0
|
11.7
|
1.0
|
N3
|
A:DC3
|
3.0
|
8.1
|
1.0
|
O2
|
A:DC4
|
3.0
|
14.5
|
1.0
|
C2
|
B:DC3
|
3.1
|
21.9
|
1.0
|
AG
|
B:AG102
|
3.1
|
14.2
|
1.0
|
AG
|
A:AG102
|
3.1
|
10.1
|
1.0
|
C4
|
B:DC3
|
3.1
|
16.4
|
1.0
|
O2
|
B:DC3
|
3.2
|
27.7
|
1.0
|
N4
|
B:DC3
|
3.2
|
18.3
|
1.0
|
N6
|
B:DA2
|
3.4
|
12.7
|
1.0
|
O2
|
B:DC4
|
3.6
|
18.0
|
1.0
|
D1
|
B:HOH205
|
3.6
|
37.5
|
1.0
|
C2
|
A:DC4
|
3.6
|
18.6
|
1.0
|
N6
|
A:DA2
|
3.8
|
10.8
|
1.0
|
N3
|
B:DC4
|
3.8
|
6.2
|
1.0
|
N1
|
B:DA2
|
3.8
|
14.2
|
1.0
|
N3
|
A:DC4
|
3.8
|
16.4
|
1.0
|
C6
|
B:DA2
|
3.9
|
16.5
|
1.0
|
D61
|
A:DA2
|
3.9
|
12.5
|
1.0
|
C2
|
B:DC4
|
3.9
|
10.3
|
1.0
|
O
|
B:HOH205
|
4.0
|
31.6
|
1.0
|
D1
|
A:HOH202
|
4.1
|
21.0
|
1.0
|
D62
|
B:DA2
|
4.1
|
14.7
|
0.2
|
H62
|
B:DA2
|
4.1
|
14.7
|
0.8
|
O
|
A:HOH202
|
4.1
|
17.9
|
1.0
|
D41
|
B:DC3
|
4.2
|
21.4
|
1.0
|
D2
|
B:HOH205
|
4.3
|
37.5
|
1.0
|
C2
|
A:DC3
|
4.3
|
8.8
|
1.0
|
C5
|
A:DC3
|
4.3
|
7.6
|
1.0
|
N1
|
B:DC3
|
4.4
|
23.6
|
1.0
|
C6
|
A:DA2
|
4.5
|
8.2
|
1.0
|
H1'
|
A:DC4
|
4.5
|
8.6
|
1.0
|
C5
|
B:DC3
|
4.5
|
22.1
|
1.0
|
N1
|
A:DC4
|
4.7
|
12.5
|
1.0
|
C4
|
B:DC4
|
4.7
|
19.4
|
1.0
|
H5
|
A:DC3
|
4.8
|
8.7
|
1.0
|
D42
|
B:DC4
|
4.8
|
19.9
|
1.0
|
C2
|
B:DA2
|
4.8
|
11.8
|
1.0
|
O2
|
A:DC3
|
4.9
|
10.9
|
1.0
|
C4
|
A:DC4
|
4.9
|
23.1
|
1.0
|
C6
|
B:DC3
|
5.0
|
15.9
|
1.0
|
|
Silver binding site 10 out
of 11 in 8dyk
Go back to
Silver Binding Sites List in 8dyk
Silver binding site 10 out
of 11 in the Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 10 of Room Temperature Neutron Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag102
b:14.2
occ:1.00
|
N6
|
A:DA2
|
2.1
|
10.8
|
1.0
|
N1
|
B:DA2
|
2.1
|
14.2
|
1.0
|
D61
|
A:DA2
|
2.7
|
12.5
|
1.0
|
C6
|
B:DA2
|
3.0
|
16.5
|
1.0
|
C6
|
A:DA2
|
3.0
|
8.2
|
1.0
|
AG
|
A:AG106
|
3.0
|
12.4
|
1.0
|
AG
|
A:AG103
|
3.0
|
7.7
|
1.0
|
N6
|
B:DA2
|
3.0
|
12.7
|
1.0
|
C2
|
B:DA2
|
3.1
|
11.8
|
1.0
|
AG
|
B:AG101
|
3.1
|
2.4
|
1.0
|
H2
|
B:DA2
|
3.1
|
13.7
|
1.0
|
N1
|
A:DA2
|
3.2
|
2.4
|
1.0
|
O2
|
B:DC3
|
3.4
|
27.7
|
1.0
|
AG
|
A:AG105
|
3.4
|
6.5
|
1.0
|
D61
|
A:DA1
|
3.6
|
22.6
|
1.0
|
C2
|
B:DC3
|
3.8
|
21.9
|
1.0
|
N3
|
B:DC3
|
3.8
|
20.3
|
1.0
|
N6
|
A:DA1
|
3.9
|
19.2
|
1.0
|
N3
|
A:DC3
|
4.0
|
8.1
|
1.0
|
N4
|
A:DC3
|
4.0
|
15.2
|
1.0
|
D62
|
B:DA2
|
4.1
|
14.7
|
0.2
|
H62
|
B:DA2
|
4.1
|
14.7
|
0.8
|
D2
|
B:HOH205
|
4.1
|
37.5
|
1.0
|
N1
|
A:DA1
|
4.1
|
17.2
|
1.0
|
O
|
B:HOH205
|
4.1
|
31.6
|
1.0
|
C6
|
A:DA1
|
4.2
|
15.2
|
1.0
|
D2
|
A:HOH206
|
4.2
|
5.7
|
0.5
|
C5
|
A:DA2
|
4.3
|
7.9
|
1.0
|
C5
|
B:DA2
|
4.3
|
7.8
|
1.0
|
N3
|
B:DA2
|
4.4
|
9.6
|
1.0
|
C4
|
A:DC3
|
4.4
|
11.7
|
1.0
|
D62
|
A:DA1
|
4.5
|
22.6
|
1.0
|
D1
|
B:HOH205
|
4.5
|
37.5
|
1.0
|
C2
|
A:DA2
|
4.5
|
14.1
|
1.0
|
O
|
A:HOH205
|
4.6
|
27.3
|
0.7
|
D1
|
A:HOH206
|
4.7
|
5.7
|
0.5
|
D2
|
A:HOH205
|
4.7
|
32.3
|
0.7
|
H1'
|
B:DC3
|
4.7
|
27.8
|
1.0
|
O
|
A:HOH206
|
4.7
|
5.2
|
0.5
|
N1
|
B:DC3
|
4.8
|
23.6
|
1.0
|
D41
|
A:DC3
|
4.8
|
17.8
|
1.0
|
C4
|
B:DC3
|
4.8
|
16.4
|
1.0
|
C4
|
B:DA2
|
4.8
|
22.9
|
1.0
|
C2
|
A:DA1
|
4.9
|
17.9
|
1.0
|
C2
|
A:DC3
|
5.0
|
8.8
|
1.0
|
|
Reference:
F.David,
C.Setzler,
A.Sorescu,
R.L.Lieberman,
F.Meilleur,
J.T.Petty.
Mapping H + in the Nanoscale (A 2 C 4 ) 2 -Ag 8 Fluorophore. J Phys Chem Lett V. 13 11317 2022.
ISSN: ESSN 1948-7185
PubMed: 36453924
DOI: 10.1021/ACS.JPCLETT.2C03161
Page generated: Wed Jul 10 09:18:51 2024
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