Silver in PDB 6niz: Atomic Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
Protein crystallography data
The structure of Atomic Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold, PDB code: 6niz
was solved by
R.L.Lieberman,
D.J.E.Huard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.54 /
0.93
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
33.290,
33.290,
62.010,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
8.2 /
9.1
|
Silver Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Silver atom in the Atomic Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold
(pdb code 6niz). This binding sites where shown within
5.0 Angstroms radius around Silver atom.
In total 12 binding sites of Silver where determined in the
Atomic Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold, PDB code: 6niz:
Jump to Silver binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Silver binding site 1 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 1 out
of 12 in the Atomic 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 Atomic 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:12.8
occ:0.99
|
N3
|
B:DC5
|
2.1
|
12.7
|
1.0
|
N3
|
A:DC5
|
2.2
|
12.1
|
1.0
|
H42
|
A:DC5
|
2.8
|
15.9
|
1.0
|
O2
|
B:DC5
|
2.9
|
13.8
|
1.0
|
C2
|
B:DC5
|
2.9
|
13.5
|
1.0
|
H42
|
B:DC5
|
2.9
|
15.6
|
1.0
|
H42
|
B:DC4
|
3.0
|
14.8
|
1.0
|
C2
|
A:DC5
|
3.0
|
12.3
|
1.0
|
AG
|
B:AG101
|
3.0
|
12.9
|
1.0
|
O2
|
A:DC5
|
3.1
|
12.7
|
1.0
|
AG
|
A:AG102
|
3.1
|
11.6
|
1.0
|
C4
|
A:DC5
|
3.1
|
12.8
|
1.0
|
O2
|
B:DC6
|
3.1
|
14.8
|
1.0
|
O2
|
A:DC6
|
3.2
|
12.8
|
1.0
|
C4
|
B:DC5
|
3.2
|
13.0
|
1.0
|
N4
|
A:DC5
|
3.3
|
13.2
|
1.0
|
N3
|
A:DC6
|
3.3
|
12.4
|
1.0
|
N4
|
B:DC4
|
3.4
|
12.3
|
1.0
|
N4
|
B:DC5
|
3.4
|
13.0
|
1.0
|
C2
|
A:DC6
|
3.4
|
12.2
|
1.0
|
H42
|
A:DC4
|
3.5
|
15.5
|
1.0
|
N3
|
B:DC4
|
3.6
|
11.7
|
1.0
|
C2
|
B:DC6
|
3.7
|
14.6
|
1.0
|
C4
|
B:DC4
|
3.7
|
12.1
|
1.0
|
N3
|
B:DC6
|
3.8
|
13.9
|
1.0
|
H41
|
B:DC4
|
3.8
|
14.8
|
1.0
|
N3
|
A:DC4
|
3.9
|
11.1
|
1.0
|
N4
|
A:DC4
|
4.0
|
12.9
|
1.0
|
H41
|
A:DC5
|
4.1
|
15.9
|
1.0
|
C4
|
A:DC6
|
4.2
|
13.1
|
1.0
|
H41
|
B:DC5
|
4.2
|
15.6
|
1.0
|
N1
|
B:DC5
|
4.2
|
13.9
|
1.0
|
C4
|
A:DC4
|
4.3
|
11.7
|
1.0
|
N1
|
A:DC5
|
4.3
|
12.8
|
1.0
|
H42
|
A:DC6
|
4.4
|
17.5
|
1.0
|
C5
|
A:DC5
|
4.5
|
13.3
|
1.0
|
C5
|
B:DC5
|
4.5
|
13.6
|
1.0
|
N1
|
A:DC6
|
4.6
|
12.5
|
1.0
|
H41
|
A:DC4
|
4.6
|
15.5
|
1.0
|
C2
|
B:DC4
|
4.6
|
12.4
|
1.0
|
H1'
|
B:DC6
|
4.7
|
21.8
|
1.0
|
N4
|
A:DC6
|
4.7
|
14.6
|
1.0
|
N1
|
B:DC6
|
4.7
|
16.1
|
1.0
|
C5
|
B:DC4
|
4.8
|
12.8
|
1.0
|
C4
|
B:DC6
|
4.8
|
14.5
|
1.0
|
C2
|
A:DC4
|
4.8
|
11.0
|
1.0
|
C6
|
B:DC5
|
4.9
|
13.8
|
1.0
|
C6
|
A:DC5
|
4.9
|
13.3
|
1.0
|
|
Silver binding site 2 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 2 out
of 12 in the Atomic 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 Atomic 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:11.6
occ:0.99
|
N3
|
A:DC4
|
2.1
|
11.1
|
1.0
|
N3
|
B:DC4
|
2.1
|
11.7
|
1.0
|
H42
|
A:DC4
|
2.8
|
15.5
|
1.0
|
H42
|
B:DC4
|
2.9
|
14.8
|
1.0
|
C2
|
B:DC4
|
2.9
|
12.4
|
1.0
|
C2
|
A:DC4
|
2.9
|
11.0
|
1.0
|
O2
|
B:DC4
|
2.9
|
12.8
|
1.0
|
O2
|
A:DC4
|
2.9
|
11.4
|
1.0
|
O2
|
B:DC5
|
3.1
|
13.8
|
1.0
|
AG
|
B:AG102
|
3.1
|
10.9
|
1.0
|
AG
|
A:AG101
|
3.1
|
12.8
|
1.0
|
H42
|
B:DC3
|
3.1
|
14.1
|
1.0
|
C4
|
A:DC4
|
3.1
|
11.7
|
1.0
|
C4
|
B:DC4
|
3.1
|
12.1
|
1.0
|
H41
|
A:DC3
|
3.2
|
12.7
|
1.0
|
N4
|
A:DC4
|
3.3
|
12.9
|
1.0
|
N4
|
B:DC4
|
3.3
|
12.3
|
1.0
|
N4
|
A:DC3
|
3.5
|
10.6
|
1.0
|
C2
|
B:DC5
|
3.6
|
13.5
|
1.0
|
N4
|
B:DC3
|
3.6
|
11.8
|
1.0
|
N3
|
B:DC5
|
3.6
|
12.7
|
1.0
|
N3
|
A:DC5
|
3.7
|
12.1
|
1.0
|
O2
|
A:DC5
|
3.8
|
12.7
|
1.0
|
N3
|
B:DC3
|
3.8
|
11.3
|
1.0
|
O
|
B:HOH208
|
3.9
|
15.2
|
1.0
|
C2
|
A:DC5
|
3.9
|
12.3
|
1.0
|
C4
|
B:DC3
|
4.0
|
11.6
|
1.0
|
H41
|
B:DC3
|
4.1
|
14.1
|
1.0
|
H41
|
A:DC4
|
4.2
|
15.5
|
1.0
|
H41
|
B:DC4
|
4.2
|
14.8
|
1.0
|
N1
|
A:DC4
|
4.2
|
11.2
|
1.0
|
N1
|
B:DC4
|
4.2
|
12.9
|
1.0
|
C4
|
A:DC3
|
4.3
|
10.1
|
1.0
|
C5
|
B:DC4
|
4.5
|
12.8
|
1.0
|
C5
|
A:DC4
|
4.5
|
12.0
|
1.0
|
C4
|
A:DC5
|
4.5
|
12.8
|
1.0
|
H42
|
A:DC5
|
4.5
|
15.9
|
1.0
|
N1
|
B:DC5
|
4.6
|
13.9
|
1.0
|
C4
|
B:DC5
|
4.7
|
13.0
|
1.0
|
H5
|
A:DC3
|
4.8
|
12.5
|
1.0
|
N4
|
A:DC5
|
4.8
|
13.2
|
1.0
|
C2
|
B:DC3
|
4.8
|
12.2
|
1.0
|
C6
|
B:DC4
|
4.8
|
12.9
|
1.0
|
C6
|
A:DC4
|
4.9
|
11.6
|
1.0
|
C5
|
A:DC3
|
4.9
|
10.4
|
1.0
|
H1'
|
B:DC5
|
4.9
|
18.1
|
1.0
|
N1
|
A:DC5
|
5.0
|
12.8
|
1.0
|
|
Silver binding site 3 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 3 out
of 12 in the Atomic 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 Atomic 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:10.1
occ:1.00
|
N6
|
B:DA2
|
2.1
|
10.3
|
1.0
|
N3
|
A:DC3
|
2.1
|
9.8
|
1.0
|
H62
|
B:DA2
|
2.5
|
12.4
|
1.0
|
AG
|
B:AG102
|
2.9
|
10.9
|
1.0
|
AG
|
B:AG103
|
2.9
|
10.6
|
1.0
|
C2
|
A:DC3
|
3.0
|
9.9
|
1.0
|
O2
|
A:DC3
|
3.0
|
10.5
|
1.0
|
C4
|
A:DC3
|
3.1
|
10.1
|
1.0
|
C6
|
B:DA2
|
3.2
|
10.5
|
1.0
|
H1'
|
A:DC4
|
3.2
|
14.8
|
1.0
|
N4
|
A:DC3
|
3.2
|
10.6
|
1.0
|
O
|
A:HOH202
|
3.3
|
10.2
|
0.5
|
H2
|
B:DA1
|
3.3
|
11.9
|
1.0
|
AG
|
A:AG106
|
3.4
|
10.2
|
1.0
|
O2
|
A:DC4
|
3.4
|
11.4
|
1.0
|
N1
|
B:DA2
|
3.5
|
10.6
|
1.0
|
N6
|
A:DA2
|
3.6
|
10.2
|
1.0
|
N1
|
A:DA2
|
3.6
|
9.8
|
1.0
|
H42
|
B:DC3
|
3.7
|
14.1
|
1.0
|
C6
|
A:DA2
|
3.7
|
9.8
|
1.0
|
C2
|
B:DA1
|
3.9
|
9.9
|
1.0
|
N3
|
B:DC3
|
4.0
|
11.3
|
1.0
|
H62
|
A:DA2
|
4.0
|
12.3
|
1.0
|
C2
|
A:DC4
|
4.1
|
11.0
|
1.0
|
H41
|
A:DC3
|
4.1
|
12.7
|
1.0
|
C1'
|
A:DC4
|
4.1
|
12.3
|
1.0
|
N4
|
B:DC3
|
4.3
|
11.8
|
1.0
|
N1
|
A:DC3
|
4.3
|
10.3
|
1.0
|
N3
|
B:DA1
|
4.4
|
10.4
|
1.0
|
N1
|
A:DC4
|
4.4
|
11.2
|
1.0
|
C2
|
A:DA2
|
4.4
|
10.0
|
1.0
|
C5
|
A:DC3
|
4.4
|
10.4
|
1.0
|
C5
|
B:DA2
|
4.5
|
10.8
|
1.0
|
C4
|
B:DC3
|
4.5
|
11.6
|
1.0
|
C5
|
A:DA2
|
4.6
|
10.3
|
1.0
|
H2
|
A:DA2
|
4.7
|
12.0
|
1.0
|
N1
|
B:DA1
|
4.7
|
10.2
|
1.0
|
O4'
|
A:DC4
|
4.8
|
11.9
|
1.0
|
C2
|
B:DC3
|
4.8
|
12.2
|
1.0
|
C2
|
B:DA2
|
4.8
|
11.3
|
1.0
|
C6
|
A:DC3
|
4.9
|
10.5
|
1.0
|
H41
|
B:DC3
|
4.9
|
14.1
|
1.0
|
O2
|
B:DC3
|
4.9
|
12.8
|
1.0
|
N3
|
A:DC4
|
4.9
|
11.1
|
1.0
|
|
Silver binding site 4 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 4 out
of 12 in the Atomic 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 Atomic 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:13.9
occ:0.50
|
N7
|
A:DA2
|
2.2
|
10.8
|
1.0
|
O
|
B:HOH210
|
2.6
|
18.4
|
1.0
|
O
|
B:HOH208
|
2.8
|
15.2
|
1.0
|
H62
|
A:DA2
|
2.9
|
12.3
|
1.0
|
H41
|
A:DC3
|
3.0
|
12.7
|
1.0
|
C8
|
A:DA2
|
3.1
|
11.1
|
1.0
|
H8
|
A:DA2
|
3.2
|
13.3
|
1.0
|
C5
|
A:DA2
|
3.3
|
10.3
|
1.0
|
N4
|
A:DC3
|
3.4
|
10.6
|
1.0
|
N6
|
A:DA2
|
3.6
|
10.2
|
1.0
|
N7
|
A:DA1
|
3.7
|
14.1
|
1.0
|
H5
|
A:DC3
|
3.8
|
12.5
|
1.0
|
C8
|
A:DA1
|
3.8
|
14.4
|
1.0
|
H2'
|
A:DA1
|
3.8
|
20.6
|
1.0
|
C6
|
A:DA2
|
3.9
|
9.8
|
1.0
|
H8
|
A:DA1
|
4.0
|
17.3
|
1.0
|
C4
|
A:DC3
|
4.0
|
10.1
|
1.0
|
H3'
|
A:DA1
|
4.0
|
21.1
|
1.0
|
C5
|
A:DA1
|
4.1
|
12.9
|
1.0
|
C5
|
A:DC3
|
4.1
|
10.4
|
1.0
|
N9
|
A:DA1
|
4.2
|
14.2
|
1.0
|
O2
|
B:DC4
|
4.2
|
12.8
|
1.0
|
OP2
|
A:DA2
|
4.2
|
18.0
|
1.0
|
O
|
A:HOH203
|
4.3
|
29.0
|
1.0
|
H4'
|
B:DC5
|
4.3
|
20.4
|
1.0
|
N9
|
A:DA2
|
4.3
|
10.8
|
1.0
|
C4
|
A:DA1
|
4.3
|
12.7
|
1.0
|
C4
|
A:DA2
|
4.4
|
10.2
|
1.0
|
H5'
|
B:DC5
|
4.5
|
21.2
|
1.0
|
C2'
|
A:DA1
|
4.6
|
17.1
|
1.0
|
AG
|
B:AG102
|
4.7
|
10.9
|
1.0
|
C6
|
A:DA1
|
4.7
|
12.5
|
1.0
|
C3'
|
A:DA1
|
4.7
|
17.5
|
1.0
|
H1'
|
B:DC4
|
4.8
|
17.0
|
1.0
|
C1'
|
A:DA1
|
5.0
|
16.3
|
1.0
|
H62
|
A:DA1
|
5.0
|
16.2
|
1.0
|
|
Silver binding site 5 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 5 out
of 12 in the Atomic 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 Atomic 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:11.3
occ:0.94
|
N1
|
A:DA1
|
2.1
|
11.7
|
1.0
|
H61
|
A:DA1
|
2.6
|
16.2
|
1.0
|
AG
|
A:AG106
|
2.9
|
10.2
|
1.0
|
C6
|
A:DA1
|
3.0
|
12.5
|
1.0
|
H2
|
A:DA1
|
3.1
|
14.3
|
1.0
|
N6
|
A:DA1
|
3.1
|
13.5
|
1.0
|
C2
|
A:DA1
|
3.1
|
11.9
|
1.0
|
AG
|
B:AG103
|
3.2
|
10.6
|
1.0
|
O
|
A:HOH208
|
3.3
|
21.9
|
1.0
|
N6
|
A:DA2
|
3.6
|
10.2
|
1.0
|
N1
|
A:DA2
|
3.8
|
9.8
|
1.0
|
H2
|
B:DA2
|
3.8
|
13.6
|
1.0
|
H62
|
A:DA1
|
3.9
|
16.2
|
1.0
|
C6
|
A:DA2
|
4.0
|
9.8
|
1.0
|
N1
|
B:DA2
|
4.1
|
10.6
|
1.0
|
H62
|
A:DA2
|
4.2
|
12.3
|
1.0
|
C2
|
B:DA2
|
4.2
|
11.3
|
1.0
|
C5
|
A:DA1
|
4.3
|
12.9
|
1.0
|
N3
|
A:DA1
|
4.4
|
12.4
|
1.0
|
C4
|
A:DA1
|
4.8
|
12.7
|
1.0
|
C2
|
A:DA2
|
4.8
|
10.0
|
1.0
|
H2
|
A:DA2
|
5.0
|
12.0
|
1.0
|
|
Silver binding site 6 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 6 out
of 12 in the Atomic 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 Atomic 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:10.2
occ:0.99
|
N1
|
A:DA2
|
2.1
|
9.8
|
1.0
|
O
|
A:HOH202
|
2.8
|
10.2
|
0.5
|
AG
|
B:AG103
|
2.9
|
10.6
|
1.0
|
H2
|
A:DA2
|
2.9
|
12.0
|
1.0
|
AG
|
A:AG105
|
2.9
|
11.3
|
0.9
|
C2
|
A:DA2
|
3.0
|
10.0
|
1.0
|
C6
|
A:DA2
|
3.1
|
9.8
|
1.0
|
N6
|
A:DA2
|
3.3
|
10.2
|
1.0
|
AG
|
A:AG103
|
3.4
|
10.1
|
1.0
|
N1
|
B:DA2
|
3.7
|
10.6
|
1.0
|
N6
|
B:DA2
|
3.8
|
10.3
|
1.0
|
C6
|
B:DA2
|
4.1
|
10.5
|
1.0
|
N1
|
A:DA1
|
4.1
|
11.7
|
1.0
|
H62
|
A:DA2
|
4.1
|
12.3
|
1.0
|
H2
|
A:DA1
|
4.2
|
14.3
|
1.0
|
N3
|
A:DA2
|
4.3
|
10.3
|
1.0
|
H62
|
B:DA2
|
4.4
|
12.4
|
1.0
|
O2
|
A:DC3
|
4.4
|
10.5
|
1.0
|
C5
|
A:DA2
|
4.4
|
10.3
|
1.0
|
N3
|
A:DC3
|
4.4
|
9.8
|
1.0
|
H2
|
B:DA1
|
4.4
|
11.9
|
1.0
|
C2
|
A:DA1
|
4.5
|
11.9
|
1.0
|
C2
|
B:DA2
|
4.6
|
11.3
|
1.0
|
H2
|
B:DA2
|
4.7
|
13.6
|
1.0
|
C2
|
A:DC3
|
4.8
|
9.9
|
1.0
|
C4
|
A:DA2
|
4.8
|
10.2
|
1.0
|
H61
|
A:DA1
|
4.8
|
16.2
|
1.0
|
C6
|
A:DA1
|
4.9
|
12.5
|
1.0
|
|
Silver binding site 7 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 7 out
of 12 in the Atomic 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 Atomic 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:11.1
occ:0.45
|
N3
|
A:DA2
|
2.3
|
10.3
|
1.0
|
O
|
A:HOH212
|
2.4
|
13.3
|
0.5
|
H1'
|
A:DA2
|
2.7
|
14.0
|
1.0
|
H2
|
A:DA2
|
2.9
|
12.0
|
1.0
|
H5'
|
A:DC3
|
3.0
|
14.3
|
1.0
|
O4'
|
A:DC3
|
3.1
|
10.9
|
1.0
|
C2
|
A:DA2
|
3.1
|
10.0
|
1.0
|
C4
|
A:DA2
|
3.4
|
10.2
|
1.0
|
C1'
|
A:DA2
|
3.6
|
11.7
|
1.0
|
H4'
|
A:DC3
|
3.6
|
13.6
|
1.0
|
C4'
|
A:DC3
|
3.7
|
11.3
|
1.0
|
C5'
|
A:DC3
|
3.7
|
11.9
|
1.0
|
N9
|
A:DA2
|
3.9
|
10.8
|
1.0
|
C1'
|
A:DC3
|
4.2
|
10.7
|
1.0
|
O4'
|
A:DA2
|
4.2
|
12.4
|
1.0
|
H5''
|
A:DC3
|
4.3
|
14.3
|
1.0
|
N1
|
A:DA2
|
4.4
|
9.8
|
1.0
|
H1'
|
A:DC3
|
4.4
|
12.9
|
1.0
|
H2''
|
A:DA2
|
4.5
|
14.4
|
1.0
|
O2
|
A:DC3
|
4.5
|
10.5
|
1.0
|
N1
|
A:DC3
|
4.6
|
10.3
|
1.0
|
C2'
|
A:DA2
|
4.7
|
12.0
|
1.0
|
C5
|
A:DA2
|
4.7
|
10.3
|
1.0
|
O5'
|
A:DC3
|
4.7
|
12.5
|
1.0
|
C2
|
A:DC3
|
4.8
|
9.9
|
1.0
|
O
|
A:HOH204
|
4.8
|
17.4
|
1.0
|
O3'
|
A:DA2
|
4.9
|
12.4
|
1.0
|
|
Silver binding site 8 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 8 out
of 12 in the Atomic 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 Atomic 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:12.9
occ:1.00
|
N3
|
A:DC6
|
2.1
|
12.4
|
1.0
|
N3
|
B:DC6
|
2.1
|
13.9
|
1.0
|
H42
|
A:DC6
|
2.8
|
17.5
|
1.0
|
H42
|
B:DC6
|
2.8
|
17.6
|
1.0
|
C2
|
B:DC6
|
2.9
|
14.6
|
1.0
|
H42
|
B:DC5
|
2.9
|
15.6
|
1.0
|
O2
|
B:DC6
|
3.0
|
14.8
|
1.0
|
C2
|
A:DC6
|
3.0
|
12.2
|
1.0
|
AG
|
A:AG101
|
3.0
|
12.8
|
1.0
|
O2
|
A:DC6
|
3.1
|
12.8
|
1.0
|
C4
|
A:DC6
|
3.1
|
13.1
|
1.0
|
C4
|
B:DC6
|
3.2
|
14.5
|
1.0
|
N4
|
A:DC6
|
3.3
|
14.6
|
1.0
|
N4
|
B:DC6
|
3.3
|
14.7
|
1.0
|
N4
|
B:DC5
|
3.3
|
13.0
|
1.0
|
N3
|
B:DC5
|
3.5
|
12.7
|
1.0
|
C4
|
B:DC5
|
3.7
|
13.0
|
1.0
|
H41
|
B:DC5
|
3.9
|
15.6
|
1.0
|
H42
|
A:DC5
|
3.9
|
15.9
|
1.0
|
H41
|
A:DC6
|
4.1
|
17.5
|
1.0
|
N3
|
A:DC5
|
4.1
|
12.1
|
1.0
|
H41
|
B:DC6
|
4.2
|
17.6
|
1.0
|
N1
|
B:DC6
|
4.3
|
16.1
|
1.0
|
N1
|
A:DC6
|
4.3
|
12.5
|
1.0
|
N4
|
A:DC5
|
4.4
|
13.2
|
1.0
|
C5
|
A:DC6
|
4.4
|
12.8
|
1.0
|
C2
|
B:DC5
|
4.5
|
13.5
|
1.0
|
C5
|
B:DC6
|
4.5
|
15.3
|
1.0
|
C4
|
A:DC5
|
4.6
|
12.8
|
1.0
|
C5
|
B:DC5
|
4.8
|
13.6
|
1.0
|
C6
|
A:DC6
|
4.9
|
12.3
|
1.0
|
C6
|
B:DC6
|
4.9
|
16.0
|
1.0
|
O2
|
B:DC5
|
4.9
|
13.8
|
1.0
|
C2
|
A:DC5
|
4.9
|
12.3
|
1.0
|
|
Silver binding site 9 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 9 out
of 12 in the Atomic 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 Atomic 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:10.9
occ:1.00
|
N4
|
A:DC3
|
2.1
|
10.6
|
1.0
|
N3
|
B:DC3
|
2.1
|
11.3
|
1.0
|
H41
|
A:DC3
|
2.5
|
12.7
|
1.0
|
H42
|
B:DC3
|
2.8
|
14.1
|
1.0
|
AG
|
A:AG103
|
2.9
|
10.1
|
1.0
|
C2
|
B:DC3
|
2.9
|
12.2
|
1.0
|
O2
|
B:DC3
|
3.0
|
12.8
|
1.0
|
AG
|
A:AG102
|
3.1
|
11.6
|
1.0
|
AG
|
B:AG103
|
3.1
|
10.6
|
1.0
|
C4
|
B:DC3
|
3.1
|
11.6
|
1.0
|
C4
|
A:DC3
|
3.2
|
10.1
|
1.0
|
O2
|
B:DC4
|
3.2
|
12.8
|
1.0
|
O2
|
A:DC4
|
3.2
|
11.4
|
1.0
|
N4
|
B:DC3
|
3.3
|
11.8
|
1.0
|
H62
|
A:DA2
|
3.4
|
12.3
|
1.0
|
N3
|
B:DC4
|
3.4
|
11.7
|
1.0
|
N3
|
A:DC3
|
3.4
|
9.8
|
1.0
|
O
|
B:HOH210
|
3.4
|
18.4
|
1.0
|
C2
|
B:DC4
|
3.5
|
12.4
|
1.0
|
N6
|
A:DA2
|
3.6
|
10.2
|
1.0
|
N6
|
B:DA2
|
3.8
|
10.3
|
1.0
|
C2
|
A:DC4
|
3.8
|
11.0
|
1.0
|
N1
|
B:DA2
|
3.8
|
10.6
|
1.0
|
N3
|
A:DC4
|
3.9
|
11.1
|
1.0
|
C6
|
B:DA2
|
4.1
|
10.5
|
1.0
|
H41
|
B:DC3
|
4.1
|
14.1
|
1.0
|
N1
|
B:DC3
|
4.2
|
13.5
|
1.0
|
H62
|
B:DA2
|
4.3
|
12.4
|
1.0
|
O
|
B:HOH208
|
4.3
|
15.2
|
1.0
|
C4
|
B:DC4
|
4.4
|
12.1
|
1.0
|
C5
|
A:DC3
|
4.4
|
10.4
|
1.0
|
C6
|
A:DA2
|
4.4
|
9.8
|
1.0
|
C5
|
B:DC3
|
4.4
|
12.2
|
1.0
|
N1
|
B:DC4
|
4.6
|
12.9
|
1.0
|
H5
|
A:DC3
|
4.6
|
12.5
|
1.0
|
AG
|
A:AG104
|
4.7
|
13.9
|
0.5
|
H42
|
B:DC4
|
4.7
|
14.8
|
1.0
|
H1'
|
A:DC4
|
4.8
|
14.8
|
1.0
|
C2
|
A:DC3
|
4.8
|
9.9
|
1.0
|
C2
|
B:DA2
|
4.8
|
11.3
|
1.0
|
C6
|
B:DC3
|
4.8
|
13.0
|
1.0
|
N1
|
A:DC4
|
4.9
|
11.2
|
1.0
|
N4
|
B:DC4
|
4.9
|
12.3
|
1.0
|
H2
|
B:DA2
|
4.9
|
13.6
|
1.0
|
C4
|
A:DC4
|
5.0
|
11.7
|
1.0
|
|
Silver binding site 10 out
of 12 in 6niz
Go back to
Silver Binding Sites List in 6niz
Silver binding site 10 out
of 12 in the Atomic 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 Atomic Structure of A Fluorescent AG8 Cluster Templated By A Multistranded Dna Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag103
b:10.6
occ:0.99
|
N6
|
A:DA2
|
2.1
|
10.2
|
1.0
|
N1
|
B:DA2
|
2.1
|
10.6
|
1.0
|
H62
|
A:DA2
|
2.5
|
12.3
|
1.0
|
AG
|
A:AG106
|
2.9
|
10.2
|
1.0
|
H2
|
B:DA2
|
2.9
|
13.6
|
1.0
|
AG
|
A:AG103
|
2.9
|
10.1
|
1.0
|
C2
|
B:DA2
|
3.0
|
11.3
|
1.0
|
O2
|
B:DC3
|
3.0
|
12.8
|
1.0
|
C6
|
B:DA2
|
3.1
|
10.5
|
1.0
|
AG
|
B:AG102
|
3.1
|
10.9
|
1.0
|
C6
|
A:DA2
|
3.1
|
9.8
|
1.0
|
AG
|
A:AG105
|
3.2
|
11.3
|
0.9
|
N6
|
B:DA2
|
3.2
|
10.3
|
1.0
|
H61
|
A:DA1
|
3.2
|
16.2
|
1.0
|
N1
|
A:DA2
|
3.4
|
9.8
|
1.0
|
C2
|
B:DC3
|
3.5
|
12.2
|
1.0
|
N6
|
A:DA1
|
3.6
|
13.5
|
1.0
|
N3
|
B:DC3
|
3.6
|
11.3
|
1.0
|
O
|
B:HOH210
|
3.9
|
18.4
|
1.0
|
C6
|
A:DA1
|
3.9
|
12.5
|
1.0
|
N1
|
A:DA1
|
3.9
|
11.7
|
1.0
|
H62
|
A:DA1
|
3.9
|
16.2
|
1.0
|
N4
|
A:DC3
|
4.0
|
10.6
|
1.0
|
H62
|
B:DA2
|
4.1
|
12.4
|
1.0
|
N3
|
A:DC3
|
4.2
|
9.8
|
1.0
|
N3
|
B:DA2
|
4.3
|
11.5
|
1.0
|
C5
|
B:DA2
|
4.4
|
10.8
|
1.0
|
C5
|
A:DA2
|
4.4
|
10.3
|
1.0
|
O
|
A:HOH208
|
4.4
|
21.9
|
1.0
|
H1'
|
B:DC3
|
4.5
|
18.5
|
1.0
|
C4
|
A:DC3
|
4.5
|
10.1
|
1.0
|
N1
|
B:DC3
|
4.6
|
13.5
|
1.0
|
H41
|
A:DC3
|
4.6
|
12.7
|
1.0
|
C4
|
B:DC3
|
4.7
|
11.6
|
1.0
|
C2
|
A:DA2
|
4.7
|
10.0
|
1.0
|
C4
|
B:DA2
|
4.8
|
11.2
|
1.0
|
C2
|
A:DA1
|
4.8
|
11.9
|
1.0
|
O
|
A:HOH202
|
4.9
|
10.2
|
0.5
|
C5
|
A:DA1
|
4.9
|
12.9
|
1.0
|
H42
|
B:DC3
|
5.0
|
14.1
|
1.0
|
|
Reference:
D.J.E.Huard,
A.Demissie,
D.Kim,
D.Lewis,
R.M.Dickson,
J.T.Petty,
R.L.Lieberman.
Atomic Structure of A Fluorescent AG8CLUSTER Templated By A Multistranded Dna Scaffold. J.Am.Chem.Soc. V. 141 11465 2019.
ISSN: ESSN 1520-5126
PubMed: 30562465
DOI: 10.1021/JACS.8B12203
Page generated: Wed Jul 10 08:35:53 2024
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