Silver in PDB 7xlv: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
Protein crystallography data
The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant), PDB code: 7xlv
was solved by
J.Kondo,
C.Cerretani,
T.Vosch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.59 /
1.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
24.212,
41.474,
45.301,
90,
90,
90
|
R / Rfree (%)
|
10.2 /
11
|
Silver Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
19;
Binding sites:
The binding sites of Silver atom in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
(pdb code 7xlv). This binding sites where shown within
5.0 Angstroms radius around Silver atom.
In total 19 binding sites of Silver where determined in the
Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant), PDB code: 7xlv:
Jump to Silver binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Silver binding site 1 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 1 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag102
b:7.0
occ:1.00
|
N3
|
A:DC3
|
2.3
|
7.1
|
1.0
|
N1
|
B:DA2
|
2.4
|
7.8
|
1.0
|
O2
|
A:DC1
|
2.5
|
6.9
|
1.0
|
AG
|
A:AG106
|
2.7
|
6.7
|
1.0
|
AG
|
B:AG102
|
2.8
|
6.8
|
1.0
|
AG
|
B:AG101
|
2.8
|
6.9
|
1.0
|
AG
|
A:AG103
|
2.9
|
6.9
|
1.0
|
H61
|
B:DA2
|
3.0
|
8.7
|
1.0
|
H42
|
A:DC3
|
3.0
|
10.4
|
1.0
|
O2
|
A:DC3
|
3.0
|
8.3
|
1.0
|
C2
|
A:DC3
|
3.1
|
8.3
|
1.0
|
H2
|
B:DA2
|
3.1
|
7.5
|
1.0
|
C2
|
B:DA2
|
3.2
|
6.2
|
1.0
|
C4
|
A:DC3
|
3.3
|
7.3
|
1.0
|
C6
|
B:DA2
|
3.3
|
6.5
|
1.0
|
C2
|
A:DC1
|
3.4
|
6.6
|
1.0
|
N6
|
B:DA2
|
3.5
|
7.2
|
1.0
|
N4
|
A:DC3
|
3.5
|
8.7
|
1.0
|
N3
|
A:DC1
|
3.7
|
6.5
|
1.0
|
O6
|
A:DG9
|
3.8
|
7.8
|
1.0
|
N3
|
A:DC4
|
4.0
|
7.6
|
1.0
|
AG
|
B:AG105
|
4.0
|
6.5
|
1.0
|
H2'
|
A:DA2
|
4.2
|
11.6
|
1.0
|
H42
|
A:DC4
|
4.3
|
9.8
|
1.0
|
H8
|
A:DA2
|
4.3
|
10.3
|
1.0
|
O2
|
B:DC1
|
4.3
|
6.9
|
1.0
|
H62
|
B:DA2
|
4.3
|
8.7
|
1.0
|
H41
|
A:DC3
|
4.3
|
10.4
|
1.0
|
O2
|
B:DC3
|
4.4
|
8.8
|
1.0
|
N3
|
B:DC1
|
4.4
|
6.7
|
1.0
|
N1
|
A:DC3
|
4.4
|
7.0
|
1.0
|
H1'
|
A:DC1
|
4.5
|
10.6
|
1.0
|
O2
|
A:DC4
|
4.5
|
7.1
|
1.0
|
C6
|
A:DG9
|
4.5
|
7.3
|
1.0
|
N3
|
B:DA2
|
4.5
|
7.5
|
1.0
|
C5
|
B:DA2
|
4.6
|
6.6
|
1.0
|
C8
|
A:DA2
|
4.6
|
8.6
|
1.0
|
C5
|
A:DC3
|
4.6
|
8.1
|
1.0
|
C2
|
A:DC4
|
4.6
|
6.1
|
1.0
|
C2
|
B:DC1
|
4.7
|
7.1
|
1.0
|
N1
|
A:DC1
|
4.7
|
6.8
|
1.0
|
N3
|
B:DC3
|
4.8
|
7.8
|
1.0
|
N4
|
A:DC4
|
4.8
|
8.2
|
1.0
|
C4
|
A:DC4
|
4.8
|
7.4
|
1.0
|
N7
|
A:DA2
|
5.0
|
9.3
|
1.0
|
C4
|
B:DA2
|
5.0
|
8.3
|
1.0
|
|
Silver binding site 2 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 2 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag103
b:6.9
occ:1.00
|
N3
|
A:DC4
|
2.4
|
7.6
|
1.0
|
O6
|
A:DG9
|
2.4
|
7.8
|
1.0
|
AG
|
B:AG102
|
2.7
|
6.8
|
1.0
|
AG
|
B:AG105
|
2.8
|
6.5
|
1.0
|
AG
|
A:AG107
|
2.8
|
6.9
|
1.0
|
AG
|
A:AG102
|
2.9
|
7.0
|
1.0
|
AG
|
A:AG106
|
2.9
|
6.7
|
1.0
|
AG
|
A:AG104
|
3.0
|
7.2
|
1.0
|
H42
|
A:DC4
|
3.0
|
9.8
|
1.0
|
AG
|
B:AG103
|
3.1
|
7.1
|
1.0
|
C2
|
A:DC4
|
3.1
|
6.1
|
1.0
|
O2
|
A:DC4
|
3.2
|
7.1
|
1.0
|
C6
|
A:DG9
|
3.3
|
7.3
|
1.0
|
C4
|
A:DC4
|
3.4
|
7.4
|
1.0
|
N4
|
A:DC4
|
3.5
|
8.2
|
1.0
|
N1
|
A:DG9
|
3.6
|
7.6
|
1.0
|
N3
|
A:DC3
|
3.8
|
7.1
|
1.0
|
AG
|
B:AG101
|
3.9
|
6.9
|
1.0
|
H42
|
A:DC3
|
4.1
|
10.4
|
1.0
|
AG
|
B:AG106
|
4.1
|
6.9
|
1.0
|
O2
|
A:DC1
|
4.2
|
6.9
|
1.0
|
O2
|
B:DC4
|
4.3
|
7.2
|
1.0
|
C4
|
A:DC3
|
4.3
|
7.3
|
1.0
|
C2
|
A:DC3
|
4.3
|
8.3
|
1.0
|
N3
|
A:DC8
|
4.3
|
7.8
|
1.0
|
H41
|
A:DC4
|
4.4
|
9.8
|
1.0
|
N4
|
A:DC3
|
4.4
|
8.7
|
1.0
|
O2
|
A:DC3
|
4.5
|
8.3
|
1.0
|
N1
|
A:DC4
|
4.5
|
6.8
|
1.0
|
N3
|
A:DC1
|
4.5
|
6.5
|
1.0
|
O6
|
B:DG9
|
4.6
|
7.9
|
1.0
|
C5
|
A:DG9
|
4.7
|
7.1
|
1.0
|
C5
|
A:DC4
|
4.7
|
9.1
|
1.0
|
N1
|
B:DG9
|
4.7
|
6.6
|
1.0
|
C2
|
A:DC8
|
4.7
|
7.5
|
1.0
|
AG
|
A:AG110
|
4.8
|
8.6
|
0.3
|
O2
|
A:DC8
|
4.8
|
9.0
|
1.0
|
C2
|
A:DC1
|
4.8
|
6.6
|
1.0
|
H42
|
A:DC8
|
4.8
|
11.2
|
1.0
|
H42
|
B:DC1
|
4.8
|
9.2
|
1.0
|
N3
|
B:DC4
|
4.9
|
7.1
|
1.0
|
C4
|
A:DC8
|
4.9
|
7.6
|
1.0
|
C2
|
A:DG9
|
5.0
|
7.1
|
1.0
|
|
Silver binding site 3 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 3 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag104
b:7.2
occ:1.00
|
N3
|
A:DC8
|
2.3
|
7.8
|
1.0
|
AG
|
B:AG103
|
2.7
|
7.1
|
1.0
|
AG
|
A:AG107
|
2.7
|
6.9
|
1.0
|
AG
|
B:AG106
|
2.8
|
6.9
|
1.0
|
AG
|
B:AG108
|
2.8
|
7.1
|
1.0
|
AG
|
A:AG108
|
2.9
|
7.4
|
1.0
|
H42
|
A:DC8
|
2.9
|
11.2
|
1.0
|
AG
|
A:AG110
|
3.0
|
8.6
|
0.3
|
AG
|
A:AG103
|
3.0
|
6.9
|
1.0
|
C2
|
A:DC8
|
3.0
|
7.5
|
1.0
|
O2
|
A:DC8
|
3.0
|
9.0
|
1.0
|
C4
|
A:DC8
|
3.2
|
7.6
|
1.0
|
AG
|
A:AG105
|
3.3
|
7.5
|
1.0
|
N4
|
A:DC8
|
3.4
|
9.4
|
1.0
|
N3
|
A:DC4
|
3.6
|
7.6
|
1.0
|
AG
|
B:AG105
|
3.9
|
6.5
|
1.0
|
O6
|
A:DG9
|
3.9
|
7.8
|
1.0
|
C2
|
A:DC4
|
3.9
|
6.1
|
1.0
|
O2
|
A:DC4
|
4.1
|
7.1
|
1.0
|
C4
|
A:DC4
|
4.2
|
7.4
|
1.0
|
H41
|
A:DC8
|
4.2
|
11.2
|
1.0
|
N1
|
A:DG9
|
4.3
|
7.6
|
1.0
|
N1
|
A:DC8
|
4.3
|
10.2
|
1.0
|
H42
|
A:DC4
|
4.3
|
9.8
|
1.0
|
AG
|
B:AG109
|
4.5
|
8.0
|
0.3
|
C5
|
A:DC8
|
4.5
|
8.5
|
1.0
|
C6
|
A:DG9
|
4.5
|
7.3
|
1.0
|
N4
|
A:DC4
|
4.5
|
8.2
|
1.0
|
OP1
|
A:DA6
|
4.6
|
8.1
|
1.0
|
AG
|
B:AG107
|
4.6
|
7.4
|
1.0
|
O2
|
B:DC8
|
4.6
|
9.1
|
1.0
|
H22
|
B:DG9
|
4.7
|
11.3
|
1.0
|
N1
|
A:DC4
|
4.8
|
6.8
|
1.0
|
N7
|
A:DI7
|
4.8
|
7.9
|
1.0
|
N3
|
B:DC8
|
4.9
|
8.2
|
1.0
|
AG
|
B:AG102
|
4.9
|
6.8
|
1.0
|
C6
|
A:DC8
|
4.9
|
8.8
|
1.0
|
|
Silver binding site 4 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 4 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag105
b:7.5
occ:1.00
|
N7
|
A:DI7
|
2.4
|
7.9
|
1.0
|
OP1
|
A:DA6
|
2.4
|
8.1
|
1.0
|
AG
|
A:AG108
|
2.7
|
7.4
|
1.0
|
AG
|
B:AG104
|
2.8
|
7.8
|
1.0
|
AG
|
B:AG108
|
2.8
|
7.1
|
1.0
|
AG
|
A:AG109
|
2.8
|
7.8
|
1.0
|
N3
|
A:DC8
|
2.9
|
7.8
|
1.0
|
AG
|
A:AG104
|
3.3
|
7.2
|
1.0
|
P
|
A:DA6
|
3.3
|
8.2
|
1.0
|
C8
|
A:DI7
|
3.3
|
7.4
|
1.0
|
C2
|
A:DC8
|
3.4
|
7.5
|
1.0
|
C5
|
A:DI7
|
3.4
|
7.9
|
1.0
|
H8
|
A:DI7
|
3.4
|
8.9
|
1.0
|
O2
|
A:DC8
|
3.5
|
9.0
|
1.0
|
OP2
|
A:DA6
|
3.5
|
10.0
|
1.0
|
H42
|
A:DC8
|
3.6
|
11.2
|
1.0
|
C4
|
A:DC8
|
3.6
|
7.6
|
1.0
|
O6
|
A:DI7
|
3.7
|
8.2
|
1.0
|
H8
|
A:DA6
|
3.7
|
9.9
|
1.0
|
AG
|
B:AG107
|
3.8
|
7.4
|
1.0
|
N4
|
A:DC8
|
3.9
|
9.4
|
1.0
|
O5'
|
A:DA6
|
3.9
|
8.6
|
1.0
|
N7
|
A:DA6
|
4.0
|
9.2
|
1.0
|
C6
|
A:DI7
|
4.0
|
8.9
|
1.0
|
C8
|
A:DA6
|
4.1
|
8.2
|
1.0
|
AG
|
A:AG110
|
4.1
|
8.6
|
0.3
|
O6
|
B:DI7
|
4.3
|
8.3
|
1.0
|
N9
|
A:DI7
|
4.5
|
10.1
|
1.0
|
N1
|
A:DC8
|
4.5
|
10.2
|
1.0
|
C4
|
A:DI7
|
4.5
|
10.6
|
1.0
|
AG
|
B:AG106
|
4.5
|
6.9
|
1.0
|
H41
|
A:DC8
|
4.6
|
11.2
|
1.0
|
O
|
A:HOH214
|
4.6
|
10.4
|
1.0
|
C5
|
A:DC8
|
4.7
|
8.5
|
1.0
|
O3'
|
A:DT5
|
4.7
|
10.8
|
1.0
|
H2''
|
A:DT5
|
4.8
|
14.5
|
1.0
|
H3'
|
A:DT5
|
4.9
|
14.0
|
1.0
|
N7
|
B:DA6
|
4.9
|
8.3
|
1.0
|
H62
|
B:DA6
|
4.9
|
13.7
|
1.0
|
|
Silver binding site 5 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 5 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag106
b:6.7
occ:1.00
|
N3
|
A:DC1
|
2.3
|
6.5
|
1.0
|
O2
|
B:DC4
|
2.5
|
7.2
|
1.0
|
O2
|
B:DC3
|
2.6
|
8.8
|
1.0
|
AG
|
A:AG102
|
2.7
|
7.0
|
1.0
|
AG
|
B:AG105
|
2.8
|
6.5
|
1.0
|
AG
|
B:AG101
|
2.8
|
6.9
|
1.0
|
H42
|
A:DC1
|
2.8
|
9.2
|
1.0
|
AG
|
A:AG103
|
2.9
|
6.9
|
1.0
|
C2
|
A:DC1
|
3.1
|
6.6
|
1.0
|
O2
|
A:DC1
|
3.1
|
6.9
|
1.0
|
AG
|
A:AG107
|
3.1
|
6.9
|
1.0
|
H2
|
B:DA2
|
3.2
|
7.5
|
1.0
|
C2
|
B:DC4
|
3.3
|
7.2
|
1.0
|
C4
|
A:DC1
|
3.3
|
7.3
|
1.0
|
N1
|
A:DG9
|
3.4
|
7.6
|
1.0
|
N4
|
A:DC1
|
3.4
|
7.7
|
1.0
|
O6
|
A:DG9
|
3.4
|
7.8
|
1.0
|
N3
|
B:DC4
|
3.4
|
7.1
|
1.0
|
C6
|
A:DG9
|
3.5
|
7.3
|
1.0
|
C2
|
B:DC3
|
3.5
|
7.1
|
1.0
|
C2
|
B:DA2
|
3.7
|
6.2
|
1.0
|
N3
|
B:DC3
|
3.8
|
7.8
|
1.0
|
N1
|
B:DA2
|
3.9
|
7.8
|
1.0
|
AG
|
B:AG102
|
3.9
|
6.8
|
1.0
|
C2
|
A:DG9
|
4.2
|
7.1
|
1.0
|
H41
|
A:DC1
|
4.2
|
9.2
|
1.0
|
H42
|
A:DC3
|
4.4
|
10.4
|
1.0
|
H22
|
A:DG9
|
4.4
|
9.9
|
1.0
|
N1
|
A:DC1
|
4.4
|
6.8
|
1.0
|
C5
|
A:DG9
|
4.5
|
7.1
|
1.0
|
N1
|
B:DC4
|
4.5
|
6.8
|
1.0
|
H1'
|
B:DC4
|
4.6
|
10.5
|
1.0
|
H1'
|
B:DC3
|
4.6
|
11.2
|
1.0
|
C5
|
A:DC1
|
4.6
|
7.6
|
1.0
|
N2
|
A:DG9
|
4.6
|
8.2
|
1.0
|
C4
|
B:DC4
|
4.7
|
7.6
|
1.0
|
N3
|
B:DA2
|
4.7
|
7.5
|
1.0
|
N1
|
B:DC3
|
4.8
|
8.9
|
1.0
|
N3
|
A:DC3
|
4.8
|
7.1
|
1.0
|
O6
|
B:DG9
|
4.8
|
7.9
|
1.0
|
AG
|
B:AG106
|
4.9
|
6.9
|
1.0
|
H42
|
A:DC4
|
4.9
|
9.8
|
1.0
|
|
Silver binding site 6 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 6 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag107
b:6.9
occ:1.00
|
N1
|
A:DG9
|
2.3
|
7.6
|
1.0
|
O2
|
B:DC4
|
2.5
|
7.2
|
1.0
|
H22
|
A:DG9
|
2.7
|
9.9
|
1.0
|
AG
|
B:AG106
|
2.7
|
6.9
|
1.0
|
AG
|
A:AG104
|
2.7
|
7.2
|
1.0
|
AG
|
A:AG103
|
2.8
|
6.9
|
1.0
|
AG
|
B:AG105
|
2.9
|
6.5
|
1.0
|
AG
|
B:AG109
|
2.9
|
8.0
|
0.3
|
C6
|
A:DG9
|
3.1
|
7.3
|
1.0
|
AG
|
A:AG106
|
3.1
|
6.7
|
1.0
|
O6
|
A:DG9
|
3.2
|
7.8
|
1.0
|
C2
|
A:DG9
|
3.2
|
7.1
|
1.0
|
AG
|
A:AG108
|
3.2
|
7.4
|
1.0
|
N2
|
A:DG9
|
3.2
|
8.2
|
1.0
|
O2
|
A:DC8
|
3.2
|
9.0
|
1.0
|
C2
|
B:DC4
|
3.4
|
7.2
|
1.0
|
N3
|
B:DC4
|
3.8
|
7.1
|
1.0
|
AG
|
B:AG103
|
3.9
|
7.1
|
1.0
|
C2
|
A:DC8
|
3.9
|
7.5
|
1.0
|
H42
|
A:DC1
|
4.0
|
9.2
|
1.0
|
H21
|
A:DG9
|
4.1
|
9.9
|
1.0
|
N3
|
A:DC8
|
4.1
|
7.8
|
1.0
|
H1'
|
B:DC4
|
4.1
|
10.5
|
1.0
|
H42
|
B:DC8
|
4.3
|
10.1
|
1.0
|
C5
|
A:DG9
|
4.4
|
7.1
|
1.0
|
N1
|
B:DC4
|
4.4
|
6.8
|
1.0
|
N3
|
A:DG9
|
4.5
|
7.4
|
1.0
|
N3
|
A:DC1
|
4.5
|
6.5
|
1.0
|
N4
|
A:DC1
|
4.6
|
7.7
|
1.0
|
H42
|
A:DC4
|
4.7
|
9.8
|
1.0
|
C1'
|
B:DC4
|
4.8
|
8.8
|
1.0
|
AG
|
B:AG108
|
4.8
|
7.1
|
1.0
|
N3
|
B:DC8
|
4.8
|
8.2
|
1.0
|
N3
|
A:DC4
|
4.8
|
7.6
|
1.0
|
C4
|
A:DG9
|
4.9
|
8.1
|
1.0
|
AG
|
B:AG102
|
5.0
|
6.8
|
1.0
|
C4
|
B:DC4
|
5.0
|
7.6
|
1.0
|
H1'
|
A:DC8
|
5.0
|
12.0
|
1.0
|
|
Silver binding site 7 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 7 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag108
b:7.4
occ:1.00
|
AG
|
B:AG109
|
2.5
|
8.0
|
0.3
|
O6
|
A:DI7
|
2.6
|
8.2
|
1.0
|
O2
|
A:DC8
|
2.7
|
9.0
|
1.0
|
AG
|
A:AG105
|
2.7
|
7.5
|
1.0
|
AG
|
B:AG106
|
2.8
|
6.9
|
1.0
|
AG
|
A:AG109
|
2.8
|
7.8
|
1.0
|
AG
|
B:AG107
|
2.9
|
7.4
|
1.0
|
AG
|
A:AG104
|
2.9
|
7.2
|
1.0
|
AG
|
B:AG108
|
3.2
|
7.1
|
1.0
|
AG
|
A:AG107
|
3.2
|
6.9
|
1.0
|
C6
|
A:DI7
|
3.5
|
8.9
|
1.0
|
C2
|
A:DC8
|
3.5
|
7.5
|
1.0
|
N3
|
A:DC8
|
3.6
|
7.8
|
1.0
|
N7
|
A:DI7
|
3.7
|
7.9
|
1.0
|
C5
|
A:DI7
|
3.9
|
7.9
|
1.0
|
H42
|
B:DC8
|
4.0
|
10.1
|
1.0
|
H22
|
A:DG9
|
4.0
|
9.9
|
1.0
|
OP2
|
B:DA6
|
4.0
|
8.7
|
1.0
|
AG
|
B:AG104
|
4.1
|
7.8
|
1.0
|
OP1
|
B:DA6
|
4.1
|
7.0
|
1.0
|
N3
|
B:DC8
|
4.3
|
8.2
|
1.0
|
H2''
|
B:DT5
|
4.6
|
13.0
|
1.0
|
P
|
B:DA6
|
4.6
|
8.1
|
1.0
|
N2
|
A:DG9
|
4.6
|
8.2
|
1.0
|
H62
|
A:DA6
|
4.6
|
14.9
|
1.0
|
N1
|
A:DG9
|
4.7
|
7.6
|
1.0
|
N1
|
A:DI7
|
4.7
|
9.7
|
1.0
|
N4
|
B:DC8
|
4.7
|
8.4
|
1.0
|
H1'
|
A:DC8
|
4.7
|
12.0
|
1.0
|
N7
|
A:DA6
|
4.8
|
9.2
|
1.0
|
AG
|
B:AG103
|
4.8
|
7.1
|
1.0
|
N1
|
A:DC8
|
4.8
|
10.2
|
1.0
|
C4
|
A:DC8
|
4.9
|
7.6
|
1.0
|
H1
|
A:DI7
|
4.9
|
11.6
|
1.0
|
O2
|
B:DC8
|
5.0
|
9.1
|
1.0
|
|
Silver binding site 8 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 8 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag109
b:7.8
occ:1.00
|
N7
|
A:DA6
|
2.3
|
9.2
|
1.0
|
OP2
|
B:DA6
|
2.3
|
8.7
|
1.0
|
O6
|
A:DI7
|
2.5
|
8.2
|
1.0
|
AG
|
B:AG104
|
2.8
|
7.8
|
1.0
|
AG
|
B:AG107
|
2.8
|
7.4
|
1.0
|
AG
|
A:AG108
|
2.8
|
7.4
|
1.0
|
AG
|
A:AG105
|
2.8
|
7.5
|
1.0
|
H62
|
A:DA6
|
2.9
|
14.9
|
1.0
|
C8
|
A:DA6
|
3.2
|
8.2
|
1.0
|
H8
|
A:DA6
|
3.2
|
9.9
|
1.0
|
C6
|
A:DI7
|
3.3
|
8.9
|
1.0
|
C5
|
A:DA6
|
3.3
|
9.2
|
1.0
|
P
|
B:DA6
|
3.4
|
8.1
|
1.0
|
H8
|
B:DA6
|
3.4
|
10.6
|
1.0
|
N7
|
A:DI7
|
3.5
|
7.9
|
1.0
|
OP1
|
B:DA6
|
3.6
|
7.0
|
1.0
|
C5
|
A:DI7
|
3.6
|
7.9
|
1.0
|
N6
|
A:DA6
|
3.7
|
12.4
|
1.0
|
N7
|
B:DA6
|
3.9
|
8.3
|
1.0
|
C6
|
A:DA6
|
3.9
|
9.2
|
1.0
|
C8
|
B:DA6
|
3.9
|
8.8
|
1.0
|
O5'
|
B:DA6
|
4.1
|
8.1
|
1.0
|
AG
|
B:AG108
|
4.1
|
7.1
|
1.0
|
H2''
|
B:DT5
|
4.3
|
13.0
|
1.0
|
N9
|
A:DA6
|
4.4
|
9.9
|
1.0
|
H61
|
A:DA6
|
4.4
|
14.9
|
1.0
|
N1
|
A:DI7
|
4.5
|
9.7
|
1.0
|
C4
|
A:DA6
|
4.5
|
9.1
|
1.0
|
AG
|
B:AG109
|
4.5
|
8.0
|
0.3
|
N7
|
B:DI7
|
4.5
|
8.0
|
1.0
|
OP2
|
A:DA6
|
4.6
|
10.0
|
1.0
|
H5'
|
B:DA6
|
4.6
|
11.2
|
1.0
|
O2
|
A:DC8
|
4.7
|
9.0
|
1.0
|
H1
|
A:DI7
|
4.7
|
11.6
|
1.0
|
C8
|
A:DI7
|
4.7
|
7.4
|
1.0
|
O3'
|
B:DT5
|
4.7
|
7.7
|
1.0
|
OP1
|
A:DA6
|
4.8
|
8.1
|
1.0
|
C4
|
A:DI7
|
4.9
|
10.6
|
1.0
|
AG
|
B:AG106
|
5.0
|
6.9
|
1.0
|
C5'
|
B:DA6
|
5.0
|
9.3
|
1.0
|
|
Silver binding site 9 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 9 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag110
b:8.6
occ:0.35
|
H42
|
A:DC8
|
2.4
|
11.2
|
1.0
|
H22
|
B:DG9
|
2.5
|
11.3
|
1.0
|
AG
|
B:AG108
|
2.6
|
7.1
|
1.0
|
AG
|
B:AG103
|
2.8
|
7.1
|
1.0
|
AG
|
A:AG104
|
3.0
|
7.2
|
1.0
|
H1'
|
A:DC4
|
3.2
|
9.9
|
1.0
|
N4
|
A:DC8
|
3.3
|
9.4
|
1.0
|
H2'
|
A:DC4
|
3.3
|
12.5
|
1.0
|
H2''
|
A:DC4
|
3.4
|
12.5
|
1.0
|
N2
|
B:DG9
|
3.4
|
9.4
|
1.0
|
O2
|
A:DC4
|
3.4
|
7.1
|
1.0
|
H2''
|
A:DT5
|
3.5
|
14.5
|
1.0
|
C2
|
A:DC4
|
3.5
|
6.1
|
1.0
|
C2'
|
A:DC4
|
3.6
|
10.4
|
1.0
|
C1'
|
A:DC4
|
3.6
|
8.3
|
1.0
|
N1
|
A:DC4
|
3.6
|
6.8
|
1.0
|
O6
|
B:DI7
|
3.6
|
8.3
|
1.0
|
H2'
|
A:DT5
|
3.6
|
14.5
|
1.0
|
H41
|
A:DC8
|
3.8
|
11.2
|
1.0
|
H21
|
B:DG9
|
3.8
|
11.3
|
1.0
|
O2
|
B:DC8
|
4.0
|
9.1
|
1.0
|
C2'
|
A:DT5
|
4.0
|
12.1
|
1.0
|
OP1
|
A:DA6
|
4.0
|
8.1
|
1.0
|
N3
|
A:DC8
|
4.1
|
7.8
|
1.0
|
AG
|
A:AG105
|
4.1
|
7.5
|
1.0
|
N1
|
B:DG9
|
4.2
|
6.6
|
1.0
|
H3'
|
A:DT5
|
4.2
|
14.0
|
1.0
|
C4
|
A:DC8
|
4.2
|
7.6
|
1.0
|
N3
|
A:DC4
|
4.2
|
7.6
|
1.0
|
AG
|
B:AG110
|
4.2
|
10.4
|
0.6
|
C2
|
B:DG9
|
4.3
|
7.4
|
1.0
|
C6
|
A:DC4
|
4.4
|
9.8
|
1.0
|
AG
|
B:AG106
|
4.4
|
6.9
|
1.0
|
C6
|
B:DI7
|
4.6
|
9.1
|
1.0
|
O
|
B:HOH230
|
4.6
|
19.1
|
1.0
|
C3'
|
A:DT5
|
4.6
|
11.7
|
1.0
|
AG
|
A:AG103
|
4.8
|
6.9
|
1.0
|
AG
|
B:AG104
|
4.8
|
7.8
|
1.0
|
P
|
A:DA6
|
4.8
|
8.2
|
1.0
|
H6
|
A:DC4
|
4.8
|
11.8
|
1.0
|
C4
|
A:DC4
|
4.8
|
7.4
|
1.0
|
OP2
|
A:DA6
|
4.9
|
10.0
|
1.0
|
H42
|
B:DC1
|
4.9
|
9.2
|
1.0
|
O4'
|
A:DC4
|
5.0
|
9.5
|
1.0
|
C5
|
A:DC4
|
5.0
|
9.1
|
1.0
|
|
Silver binding site 10 out
of 19 in 7xlv
Go back to
Silver Binding Sites List in 7xlv
Silver binding site 10 out
of 19 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant)
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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag101
b:6.9
occ:1.00
|
N3
|
B:DC3
|
2.2
|
7.8
|
1.0
|
O2
|
B:DC1
|
2.4
|
6.9
|
1.0
|
AG
|
B:AG102
|
2.7
|
6.8
|
1.0
|
AG
|
A:AG106
|
2.8
|
6.7
|
1.0
|
AG
|
B:AG105
|
2.8
|
6.5
|
1.0
|
AG
|
A:AG102
|
2.8
|
7.0
|
1.0
|
H42
|
B:DC3
|
2.9
|
10.7
|
1.0
|
N1
|
B:DA2
|
2.9
|
7.8
|
1.0
|
C2
|
B:DC3
|
3.0
|
7.1
|
1.0
|
O2
|
B:DC3
|
3.0
|
8.8
|
1.0
|
C2
|
B:DA2
|
3.2
|
6.2
|
1.0
|
C4
|
B:DC3
|
3.2
|
7.2
|
1.0
|
H2
|
B:DA2
|
3.3
|
7.5
|
1.0
|
C2
|
B:DC1
|
3.3
|
7.1
|
1.0
|
O6
|
B:DG9
|
3.4
|
7.9
|
1.0
|
C6
|
B:DA2
|
3.4
|
6.5
|
1.0
|
N4
|
B:DC3
|
3.4
|
8.9
|
1.0
|
N3
|
B:DC1
|
3.6
|
6.7
|
1.0
|
N3
|
B:DC4
|
3.7
|
7.1
|
1.0
|
H42
|
B:DC4
|
3.7
|
8.2
|
1.0
|
N3
|
B:DA2
|
3.9
|
7.5
|
1.0
|
N6
|
B:DA2
|
3.9
|
7.2
|
1.0
|
H61
|
B:DA2
|
3.9
|
8.7
|
1.0
|
AG
|
A:AG103
|
3.9
|
6.9
|
1.0
|
C5
|
B:DA2
|
4.0
|
6.6
|
1.0
|
C6
|
B:DG9
|
4.0
|
6.2
|
1.0
|
C4
|
B:DA2
|
4.2
|
8.3
|
1.0
|
H41
|
B:DC3
|
4.2
|
10.7
|
1.0
|
N4
|
B:DC4
|
4.3
|
6.8
|
1.0
|
C4
|
B:DC4
|
4.4
|
7.6
|
1.0
|
N1
|
B:DC3
|
4.4
|
8.9
|
1.0
|
O2
|
B:DC4
|
4.4
|
7.2
|
1.0
|
C2
|
B:DC4
|
4.4
|
7.2
|
1.0
|
H1'
|
B:DC1
|
4.4
|
10.6
|
1.0
|
O2
|
A:DC3
|
4.5
|
8.3
|
1.0
|
H62
|
B:DA2
|
4.5
|
8.7
|
1.0
|
C5
|
B:DC3
|
4.6
|
8.9
|
1.0
|
O2
|
A:DC1
|
4.6
|
6.9
|
1.0
|
N1
|
B:DC1
|
4.6
|
7.7
|
1.0
|
N3
|
A:DC1
|
4.6
|
6.5
|
1.0
|
C5
|
B:DG9
|
4.7
|
7.2
|
1.0
|
N1
|
B:DG9
|
4.7
|
6.6
|
1.0
|
AG
|
B:AG103
|
4.8
|
7.1
|
1.0
|
H2'
|
B:DA2
|
4.8
|
9.5
|
1.0
|
N3
|
A:DC3
|
4.9
|
7.1
|
1.0
|
C4
|
B:DC1
|
5.0
|
7.7
|
1.0
|
H41
|
B:DC4
|
5.0
|
8.2
|
1.0
|
C6
|
B:DC3
|
5.0
|
8.4
|
1.0
|
N7
|
B:DG9
|
5.0
|
9.2
|
1.0
|
C1'
|
B:DC1
|
5.0
|
8.8
|
1.0
|
|
Reference:
C.Cerretani,
M.B.Liisberg,
V.Ruck,
J.Kondo,
T.Vosch.
The Effect of Inosine on the Spectroscopic Properties and Crystal Structure of A Nir-Emitting Dna-Stabilized Silver Nanocluster. Nanoscale Adv V. 4 3212 2022.
ISSN: ESSN 2516-0230
PubMed: 36132821
DOI: 10.1039/D2NA00325B
Page generated: Wed Jul 10 09:03:09 2024
|