Silver in PDB 9gdm: Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Silver Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Silver atom in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
(pdb code 9gdm). This binding sites where shown within
5.0 Angstroms radius around Silver atom.
In total 12 binding sites of Silver where determined in the
Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions, PDB code: 9gdm:
Jump to Silver binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Silver binding site 1 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 1 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 1 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag101
b:0.0
occ:1.00
|
N1
|
B:7GU14
|
2.2
|
0.0
|
1.0
|
N3
|
A:DC11
|
2.2
|
0.0
|
1.0
|
O6
|
B:7GU14
|
2.8
|
0.0
|
1.0
|
H41
|
A:DC11
|
2.8
|
0.0
|
1.0
|
C6
|
B:7GU14
|
2.9
|
0.0
|
1.0
|
N1
|
B:7DA15
|
2.9
|
0.0
|
1.0
|
N3
|
A:DC12
|
2.9
|
0.0
|
1.0
|
O2
|
A:DC11
|
3.0
|
0.0
|
1.0
|
C2
|
A:DC11
|
3.0
|
0.0
|
1.0
|
C2
|
B:7DA15
|
3.1
|
0.0
|
1.0
|
H2
|
B:7DA15
|
3.1
|
0.0
|
1.0
|
C2
|
A:DC12
|
3.1
|
0.0
|
1.0
|
HN21
|
B:7GU14
|
3.2
|
0.0
|
1.0
|
C4
|
A:DC11
|
3.2
|
0.0
|
1.0
|
C2
|
B:7GU14
|
3.3
|
0.0
|
1.0
|
C4
|
A:DC12
|
3.4
|
0.0
|
1.0
|
N4
|
A:DC11
|
3.4
|
0.0
|
1.0
|
O2
|
A:DC12
|
3.4
|
0.0
|
1.0
|
N2
|
B:7GU14
|
3.6
|
0.0
|
1.0
|
C6
|
B:7DA15
|
3.6
|
0.0
|
1.0
|
N1
|
A:DC12
|
3.7
|
0.0
|
1.0
|
AG
|
A:AG102
|
3.9
|
0.0
|
1.0
|
N3
|
B:7DA15
|
3.9
|
0.0
|
1.0
|
AG
|
B:AG101
|
3.9
|
0.0
|
1.0
|
N4
|
A:DC12
|
3.9
|
0.0
|
1.0
|
C5
|
A:DC12
|
4.0
|
0.0
|
1.0
|
H41
|
A:DC12
|
4.0
|
0.0
|
1.0
|
C6
|
A:DC12
|
4.2
|
0.0
|
1.0
|
HN61
|
B:7DA15
|
4.2
|
0.0
|
1.0
|
N6
|
B:7DA15
|
4.2
|
0.0
|
1.0
|
C5
|
B:7GU14
|
4.3
|
0.0
|
1.0
|
C5
|
B:7DA15
|
4.3
|
0.0
|
1.0
|
N1
|
A:DC11
|
4.3
|
0.0
|
1.0
|
H42
|
A:DC11
|
4.4
|
0.0
|
1.0
|
H1'
|
A:DC12
|
4.4
|
0.0
|
1.0
|
C4
|
B:7DA15
|
4.4
|
0.0
|
1.0
|
C5
|
A:DC11
|
4.5
|
0.0
|
1.0
|
N3
|
B:7GU14
|
4.6
|
0.0
|
1.0
|
HN22
|
B:7GU14
|
4.6
|
0.0
|
1.0
|
H42
|
A:DC12
|
4.6
|
0.0
|
1.0
|
C1'
|
A:DC12
|
4.6
|
0.0
|
1.0
|
H5
|
A:DC12
|
4.7
|
0.0
|
1.0
|
O6
|
B:7GU13
|
4.9
|
0.0
|
1.0
|
C4
|
B:7GU14
|
4.9
|
0.0
|
1.0
|
C6
|
A:DC11
|
5.0
|
0.0
|
1.0
|
HN62
|
B:7DA15
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 2 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 2 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 2 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag102
b:0.0
occ:1.00
|
N3
|
A:DT10
|
2.1
|
0.0
|
1.0
|
N1
|
B:7DA15
|
2.2
|
0.0
|
1.0
|
HN61
|
B:7DA15
|
2.7
|
0.0
|
1.0
|
C4
|
A:DT10
|
3.0
|
0.0
|
1.0
|
C2
|
A:DT10
|
3.0
|
0.0
|
1.0
|
O4
|
A:DT10
|
3.1
|
0.0
|
1.0
|
C6
|
B:7DA15
|
3.1
|
0.0
|
1.0
|
N3
|
A:DC11
|
3.1
|
0.0
|
1.0
|
O2
|
A:DT10
|
3.1
|
0.0
|
1.0
|
C2
|
B:7DA15
|
3.2
|
0.0
|
1.0
|
N6
|
B:7DA15
|
3.2
|
0.0
|
1.0
|
H2
|
B:7DA15
|
3.2
|
0.0
|
1.0
|
AG
|
B:AG102
|
3.3
|
0.0
|
1.0
|
N3
|
B:DC16
|
3.4
|
0.0
|
1.0
|
C2
|
A:DC11
|
3.4
|
0.0
|
1.0
|
O2
|
B:DC16
|
3.5
|
0.0
|
1.0
|
C4
|
A:DC11
|
3.6
|
0.0
|
1.0
|
C2
|
B:DC16
|
3.6
|
0.0
|
1.0
|
O2
|
A:DC11
|
3.7
|
0.0
|
1.0
|
AG
|
A:AG101
|
3.9
|
0.0
|
1.0
|
N4
|
A:DC11
|
4.0
|
0.0
|
1.0
|
H41
|
A:DC11
|
4.0
|
0.0
|
1.0
|
N1
|
A:DC11
|
4.1
|
0.0
|
1.0
|
HN62
|
B:7DA15
|
4.2
|
0.0
|
1.0
|
C5
|
A:DC11
|
4.3
|
0.0
|
1.0
|
C4
|
B:DC16
|
4.3
|
0.0
|
1.0
|
N1
|
A:DT10
|
4.3
|
0.0
|
1.0
|
H41
|
B:DC16
|
4.4
|
0.0
|
1.0
|
C5
|
B:7DA15
|
4.4
|
0.0
|
1.0
|
C5
|
A:DT10
|
4.4
|
0.0
|
1.0
|
N3
|
B:7DA15
|
4.5
|
0.0
|
1.0
|
C6
|
A:DC11
|
4.5
|
0.0
|
1.0
|
O6
|
A:7GU9
|
4.6
|
0.0
|
1.0
|
N1
|
A:7GU9
|
4.6
|
0.0
|
1.0
|
N4
|
B:DC16
|
4.6
|
0.0
|
1.0
|
H42
|
A:DC11
|
4.7
|
0.0
|
1.0
|
N1
|
B:DC16
|
4.7
|
0.0
|
1.0
|
C6
|
A:7GU9
|
4.8
|
0.0
|
1.0
|
O6
|
B:7GU14
|
4.9
|
0.0
|
1.0
|
C6
|
A:DT10
|
4.9
|
0.0
|
1.0
|
C4
|
B:7DA15
|
4.9
|
0.0
|
1.0
|
H5
|
A:DC11
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 3 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 3 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 3 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag103
b:0.0
occ:1.00
|
N3
|
B:DT17
|
2.1
|
0.0
|
1.0
|
N1
|
A:7DA8
|
2.2
|
0.0
|
1.0
|
HN61
|
A:7DA8
|
2.6
|
0.0
|
1.0
|
N1
|
A:7GU9
|
2.8
|
0.0
|
1.0
|
C4
|
B:DT17
|
3.0
|
0.0
|
1.0
|
N3
|
B:DC18
|
3.0
|
0.0
|
1.0
|
C2
|
B:DT17
|
3.0
|
0.0
|
1.0
|
O4
|
B:DT17
|
3.1
|
0.0
|
1.0
|
HN21
|
A:7GU9
|
3.1
|
0.0
|
1.0
|
C6
|
A:7DA8
|
3.1
|
0.0
|
1.0
|
O2
|
B:DT17
|
3.1
|
0.0
|
1.0
|
C2
|
A:7GU9
|
3.2
|
0.0
|
1.0
|
N6
|
A:7DA8
|
3.2
|
0.0
|
1.0
|
C2
|
A:7DA8
|
3.2
|
0.0
|
1.0
|
C2
|
B:DC18
|
3.2
|
0.0
|
1.0
|
H2
|
A:7DA8
|
3.2
|
0.0
|
1.0
|
C6
|
A:7GU9
|
3.3
|
0.0
|
1.0
|
C4
|
B:DC18
|
3.4
|
0.0
|
1.0
|
N2
|
A:7GU9
|
3.4
|
0.0
|
1.0
|
O2
|
B:DC18
|
3.6
|
0.0
|
1.0
|
O6
|
A:7GU9
|
3.7
|
0.0
|
1.0
|
AG
|
B:AG102
|
3.7
|
0.0
|
1.0
|
N1
|
B:DC18
|
3.8
|
0.0
|
1.0
|
C5
|
B:DC18
|
4.0
|
0.0
|
1.0
|
N4
|
B:DC18
|
4.0
|
0.0
|
1.0
|
N3
|
A:7GU9
|
4.0
|
0.0
|
1.0
|
HN22
|
A:7GU9
|
4.0
|
0.0
|
1.0
|
AG
|
B:AG103
|
4.0
|
0.0
|
1.0
|
C5
|
A:7GU9
|
4.1
|
0.0
|
1.0
|
H41
|
B:DC18
|
4.1
|
0.0
|
1.0
|
C6
|
B:DC18
|
4.1
|
0.0
|
1.0
|
HN62
|
A:7DA8
|
4.2
|
0.0
|
1.0
|
N1
|
B:DT17
|
4.3
|
0.0
|
1.0
|
C4
|
A:7GU9
|
4.4
|
0.0
|
1.0
|
C5
|
A:7DA8
|
4.4
|
0.0
|
1.0
|
C5
|
B:DT17
|
4.4
|
0.0
|
1.0
|
H41
|
B:DC16
|
4.5
|
0.0
|
1.0
|
H1'
|
B:DC18
|
4.5
|
0.0
|
1.0
|
N3
|
A:7DA8
|
4.5
|
0.0
|
1.0
|
H42
|
B:DC18
|
4.6
|
0.0
|
1.0
|
C1'
|
B:DC18
|
4.6
|
0.0
|
1.0
|
H5
|
B:DC18
|
4.7
|
0.0
|
1.0
|
O6
|
A:7GU7
|
4.9
|
0.0
|
1.0
|
C6
|
B:DT17
|
4.9
|
0.0
|
1.0
|
H6
|
B:DC18
|
4.9
|
0.0
|
1.0
|
C4
|
A:7DA8
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 4 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 4 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 4 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag104
b:0.0
occ:1.00
|
N1
|
B:7GU19
|
2.2
|
0.0
|
1.0
|
N3
|
A:DC6
|
2.2
|
0.0
|
1.0
|
H41
|
A:DC6
|
2.8
|
0.0
|
1.0
|
O6
|
B:7GU19
|
2.8
|
0.0
|
1.0
|
C6
|
B:7GU19
|
2.9
|
0.0
|
1.0
|
C2
|
A:DC6
|
3.0
|
0.0
|
1.0
|
HN21
|
B:7GU19
|
3.0
|
0.0
|
1.0
|
O2
|
A:DC6
|
3.0
|
0.0
|
1.0
|
N1
|
B:7DA20
|
3.1
|
0.0
|
1.0
|
C6
|
A:7GU7
|
3.2
|
0.0
|
1.0
|
C4
|
A:DC6
|
3.2
|
0.0
|
1.0
|
C2
|
B:7DA20
|
3.2
|
0.0
|
1.0
|
N1
|
A:7GU7
|
3.2
|
0.0
|
1.0
|
H2
|
B:7DA20
|
3.3
|
0.0
|
1.0
|
C2
|
B:7GU19
|
3.3
|
0.0
|
1.0
|
N4
|
A:DC6
|
3.4
|
0.0
|
1.0
|
C5
|
A:7GU7
|
3.5
|
0.0
|
1.0
|
O6
|
A:7GU7
|
3.6
|
0.0
|
1.0
|
N2
|
B:7GU19
|
3.6
|
0.0
|
1.0
|
C2
|
A:7GU7
|
3.6
|
0.0
|
1.0
|
C6
|
B:7DA20
|
3.8
|
0.0
|
1.0
|
C4
|
A:7GU7
|
3.9
|
0.0
|
1.0
|
N3
|
B:7DA20
|
3.9
|
0.0
|
1.0
|
N3
|
A:7GU7
|
4.0
|
0.0
|
1.0
|
AG
|
A:AG105
|
4.0
|
0.0
|
1.0
|
HN21
|
A:7GU7
|
4.3
|
0.0
|
1.0
|
C7
|
A:7GU7
|
4.3
|
0.0
|
1.0
|
N2
|
A:7GU7
|
4.3
|
0.0
|
1.0
|
C5
|
B:7GU19
|
4.3
|
0.0
|
1.0
|
N1
|
A:DC6
|
4.3
|
0.0
|
1.0
|
H42
|
A:DC6
|
4.4
|
0.0
|
1.0
|
C5
|
B:7DA20
|
4.4
|
0.0
|
1.0
|
N6
|
B:7DA20
|
4.4
|
0.0
|
1.0
|
HN61
|
B:7DA20
|
4.4
|
0.0
|
1.0
|
C4
|
B:7DA20
|
4.4
|
0.0
|
1.0
|
AG
|
B:AG103
|
4.4
|
0.0
|
1.0
|
C5
|
A:DC6
|
4.5
|
0.0
|
1.0
|
HN22
|
B:7GU19
|
4.6
|
0.0
|
1.0
|
H41
|
B:DC18
|
4.6
|
0.0
|
1.0
|
N3
|
B:7GU19
|
4.6
|
0.0
|
1.0
|
H7
|
A:7GU7
|
4.7
|
0.0
|
1.0
|
N9
|
A:7GU7
|
4.7
|
0.0
|
1.0
|
HN22
|
A:7GU7
|
4.8
|
0.0
|
1.0
|
C6
|
A:DC6
|
5.0
|
0.0
|
1.0
|
C4
|
B:7GU19
|
5.0
|
0.0
|
1.0
|
C8
|
A:7GU7
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 5 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 5 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 5 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag105
b:0.0
occ:1.00
|
N3
|
A:DT5
|
2.1
|
0.0
|
1.0
|
N1
|
B:7DA20
|
2.2
|
0.0
|
1.0
|
HN61
|
B:7DA20
|
2.7
|
0.0
|
1.0
|
N1
|
B:7GU21
|
2.8
|
0.0
|
1.0
|
C4
|
A:DT5
|
3.0
|
0.0
|
1.0
|
N3
|
A:DC6
|
3.0
|
0.0
|
1.0
|
C2
|
A:DT5
|
3.0
|
0.0
|
1.0
|
HN22
|
B:7GU21
|
3.1
|
0.0
|
1.0
|
O4
|
A:DT5
|
3.1
|
0.0
|
1.0
|
C6
|
B:7DA20
|
3.1
|
0.0
|
1.0
|
C2
|
B:7GU21
|
3.1
|
0.0
|
1.0
|
O2
|
A:DT5
|
3.1
|
0.0
|
1.0
|
N6
|
B:7DA20
|
3.2
|
0.0
|
1.0
|
C2
|
B:7DA20
|
3.2
|
0.0
|
1.0
|
C2
|
A:DC6
|
3.2
|
0.0
|
1.0
|
H2
|
B:7DA20
|
3.2
|
0.0
|
1.0
|
N2
|
B:7GU21
|
3.3
|
0.0
|
1.0
|
C6
|
B:7GU21
|
3.4
|
0.0
|
1.0
|
C4
|
A:DC6
|
3.5
|
0.0
|
1.0
|
O2
|
A:DC6
|
3.5
|
0.0
|
1.0
|
AG
|
A:AG106
|
3.7
|
0.0
|
1.0
|
N1
|
A:DC6
|
3.8
|
0.0
|
1.0
|
O6
|
B:7GU21
|
3.8
|
0.0
|
1.0
|
HN21
|
B:7GU21
|
3.9
|
0.0
|
1.0
|
N3
|
B:7GU21
|
3.9
|
0.0
|
1.0
|
AG
|
A:AG104
|
4.0
|
0.0
|
1.0
|
C5
|
A:DC6
|
4.0
|
0.0
|
1.0
|
N4
|
A:DC6
|
4.0
|
0.0
|
1.0
|
C5
|
B:7GU21
|
4.1
|
0.0
|
1.0
|
H41
|
A:DC6
|
4.1
|
0.0
|
1.0
|
HN62
|
B:7DA20
|
4.2
|
0.0
|
1.0
|
C6
|
A:DC6
|
4.2
|
0.0
|
1.0
|
N1
|
A:DT5
|
4.3
|
0.0
|
1.0
|
C4
|
B:7GU21
|
4.3
|
0.0
|
1.0
|
C5
|
B:7DA20
|
4.4
|
0.0
|
1.0
|
C5
|
A:DT5
|
4.4
|
0.0
|
1.0
|
H1'
|
A:DC6
|
4.5
|
0.0
|
1.0
|
H41
|
A:DC4
|
4.5
|
0.0
|
1.0
|
N3
|
B:7DA20
|
4.5
|
0.0
|
1.0
|
C1'
|
A:DC6
|
4.7
|
0.0
|
1.0
|
H42
|
A:DC6
|
4.7
|
0.0
|
1.0
|
H5
|
A:DC6
|
4.8
|
0.0
|
1.0
|
O6
|
B:7GU19
|
4.9
|
0.0
|
1.0
|
C6
|
A:DT5
|
4.9
|
0.0
|
1.0
|
C4
|
B:7DA20
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 6 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 6 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 6 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag106
b:0.0
occ:1.00
|
N1
|
B:7GU21
|
2.2
|
0.0
|
1.0
|
N3
|
A:DC4
|
2.2
|
0.0
|
1.0
|
O6
|
B:7GU21
|
2.8
|
0.0
|
1.0
|
H41
|
A:DC4
|
2.8
|
0.0
|
1.0
|
C6
|
B:7GU21
|
2.9
|
0.0
|
1.0
|
N3
|
A:DT5
|
2.9
|
0.0
|
1.0
|
C2
|
A:DC4
|
3.0
|
0.0
|
1.0
|
O2
|
A:DC4
|
3.0
|
0.0
|
1.0
|
HN22
|
B:7GU21
|
3.1
|
0.0
|
1.0
|
C2
|
A:DT5
|
3.2
|
0.0
|
1.0
|
C4
|
A:DC4
|
3.2
|
0.0
|
1.0
|
AG
|
B:AG104
|
3.3
|
0.0
|
1.0
|
C2
|
B:7GU21
|
3.3
|
0.0
|
1.0
|
O2
|
A:DT5
|
3.4
|
0.0
|
1.0
|
N4
|
A:DC4
|
3.4
|
0.0
|
1.0
|
N3
|
B:DT22
|
3.4
|
0.0
|
1.0
|
C4
|
A:DT5
|
3.5
|
0.0
|
1.0
|
N2
|
B:7GU21
|
3.6
|
0.0
|
1.0
|
AG
|
A:AG105
|
3.7
|
0.0
|
1.0
|
O2
|
B:DT22
|
3.8
|
0.0
|
1.0
|
C2
|
B:DT22
|
3.8
|
0.0
|
1.0
|
N1
|
A:DT5
|
3.9
|
0.0
|
1.0
|
O4
|
A:DT5
|
3.9
|
0.0
|
1.0
|
C4
|
B:DT22
|
4.1
|
0.0
|
1.0
|
C5
|
A:DT5
|
4.2
|
0.0
|
1.0
|
C5
|
B:7GU21
|
4.3
|
0.0
|
1.0
|
HN62
|
A:7DA3
|
4.3
|
0.0
|
1.0
|
N1
|
A:DC4
|
4.3
|
0.0
|
1.0
|
O4
|
B:DT22
|
4.4
|
0.0
|
1.0
|
H42
|
A:DC4
|
4.4
|
0.0
|
1.0
|
C6
|
A:DT5
|
4.4
|
0.0
|
1.0
|
HN61
|
B:7DA20
|
4.4
|
0.0
|
1.0
|
C5
|
A:DC4
|
4.5
|
0.0
|
1.0
|
N1
|
A:7DA3
|
4.5
|
0.0
|
1.0
|
HN21
|
B:7GU21
|
4.6
|
0.0
|
1.0
|
N3
|
B:7GU21
|
4.6
|
0.0
|
1.0
|
N6
|
A:7DA3
|
4.6
|
0.0
|
1.0
|
H1'
|
A:DT5
|
4.7
|
0.0
|
1.0
|
C6
|
A:7DA3
|
4.8
|
0.0
|
1.0
|
C1'
|
A:DT5
|
4.8
|
0.0
|
1.0
|
N1
|
B:DT22
|
4.8
|
0.0
|
1.0
|
C4
|
B:7GU21
|
4.9
|
0.0
|
1.0
|
C6
|
A:DC4
|
5.0
|
0.0
|
1.0
|
N6
|
B:7DA20
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 7 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 7 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 7 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag107
b:0.0
occ:1.00
|
N1
|
A:7GU1
|
2.2
|
0.0
|
1.0
|
N3
|
B:DC24
|
2.2
|
0.0
|
1.0
|
O6
|
A:7GU1
|
2.8
|
0.0
|
1.0
|
C6
|
A:7GU1
|
2.9
|
0.0
|
1.0
|
H41
|
B:DC24
|
2.9
|
0.0
|
1.0
|
N1
|
A:7GU2
|
2.9
|
0.0
|
1.0
|
HN22
|
A:7GU1
|
3.0
|
0.0
|
1.0
|
C2
|
B:DC24
|
3.0
|
0.0
|
1.0
|
O2
|
B:DC24
|
3.1
|
0.0
|
1.0
|
HN21
|
A:7GU2
|
3.1
|
0.0
|
1.0
|
C4
|
B:DC24
|
3.2
|
0.0
|
1.0
|
C2
|
A:7GU2
|
3.3
|
0.0
|
1.0
|
C2
|
A:7GU1
|
3.3
|
0.0
|
1.0
|
N4
|
B:DC24
|
3.4
|
0.0
|
1.0
|
N2
|
A:7GU2
|
3.4
|
0.0
|
1.0
|
N2
|
A:7GU1
|
3.6
|
0.0
|
1.0
|
C6
|
A:7GU2
|
3.6
|
0.0
|
1.0
|
AG
|
B:AG105
|
3.8
|
0.0
|
1.0
|
O6
|
A:7GU2
|
4.0
|
0.0
|
1.0
|
HN22
|
A:7GU2
|
4.0
|
0.0
|
1.0
|
N3
|
A:7GU2
|
4.1
|
0.0
|
1.0
|
C5
|
A:7GU1
|
4.3
|
0.0
|
1.0
|
N1
|
B:DC24
|
4.3
|
0.0
|
1.0
|
C5
|
A:7GU2
|
4.4
|
0.0
|
1.0
|
H42
|
B:DC24
|
4.4
|
0.0
|
1.0
|
C5
|
B:DC24
|
4.5
|
0.0
|
1.0
|
HN21
|
A:7GU1
|
4.5
|
0.0
|
1.0
|
C4
|
A:7GU2
|
4.6
|
0.0
|
1.0
|
N3
|
A:7GU1
|
4.6
|
0.0
|
1.0
|
H41
|
B:DC23
|
4.8
|
0.0
|
1.0
|
C4
|
A:7GU1
|
4.9
|
0.0
|
1.0
|
C6
|
B:DC24
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 8 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 8 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 8 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag101
b:0.0
occ:1.00
|
N1
|
B:7GU13
|
2.2
|
0.0
|
1.0
|
N3
|
A:DC12
|
2.2
|
0.0
|
1.0
|
O6
|
B:7GU13
|
2.8
|
0.0
|
1.0
|
H41
|
A:DC12
|
2.9
|
0.0
|
1.0
|
C6
|
B:7GU13
|
2.9
|
0.0
|
1.0
|
N1
|
B:7GU14
|
3.0
|
0.0
|
1.0
|
HN21
|
B:7GU13
|
3.0
|
0.0
|
1.0
|
C2
|
A:DC12
|
3.0
|
0.0
|
1.0
|
O2
|
A:DC12
|
3.1
|
0.0
|
1.0
|
HN21
|
B:7GU14
|
3.1
|
0.0
|
1.0
|
C4
|
A:DC12
|
3.2
|
0.0
|
1.0
|
C2
|
B:7GU14
|
3.3
|
0.0
|
1.0
|
C2
|
B:7GU13
|
3.3
|
0.0
|
1.0
|
N4
|
A:DC12
|
3.4
|
0.0
|
1.0
|
N2
|
B:7GU14
|
3.4
|
0.0
|
1.0
|
N2
|
B:7GU13
|
3.6
|
0.0
|
1.0
|
C6
|
B:7GU14
|
3.6
|
0.0
|
1.0
|
AG
|
A:AG101
|
3.9
|
0.0
|
1.0
|
O6
|
B:7GU14
|
4.0
|
0.0
|
1.0
|
HN22
|
B:7GU14
|
4.0
|
0.0
|
1.0
|
N3
|
B:7GU14
|
4.1
|
0.0
|
1.0
|
C5
|
B:7GU13
|
4.3
|
0.0
|
1.0
|
C5
|
B:7GU14
|
4.3
|
0.0
|
1.0
|
N1
|
A:DC12
|
4.4
|
0.0
|
1.0
|
H42
|
A:DC12
|
4.4
|
0.0
|
1.0
|
C5
|
A:DC12
|
4.5
|
0.0
|
1.0
|
C4
|
B:7GU14
|
4.5
|
0.0
|
1.0
|
HN22
|
B:7GU13
|
4.5
|
0.0
|
1.0
|
N3
|
B:7GU13
|
4.6
|
0.0
|
1.0
|
H41
|
A:DC11
|
4.9
|
0.0
|
1.0
|
C4
|
B:7GU13
|
5.0
|
0.0
|
1.0
|
C6
|
A:DC12
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 9 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 9 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 9 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag102
b:0.0
occ:1.00
|
N1
|
A:7GU9
|
2.2
|
0.0
|
1.0
|
N3
|
B:DC16
|
2.2
|
0.0
|
1.0
|
O6
|
A:7GU9
|
2.8
|
0.0
|
1.0
|
H41
|
B:DC16
|
2.9
|
0.0
|
1.0
|
C6
|
A:7GU9
|
2.9
|
0.0
|
1.0
|
N3
|
B:DT17
|
2.9
|
0.0
|
1.0
|
C2
|
B:DC16
|
3.0
|
0.0
|
1.0
|
O2
|
B:DC16
|
3.0
|
0.0
|
1.0
|
C2
|
B:DT17
|
3.1
|
0.0
|
1.0
|
HN21
|
A:7GU9
|
3.2
|
0.0
|
1.0
|
C4
|
B:DC16
|
3.2
|
0.0
|
1.0
|
AG
|
A:AG102
|
3.3
|
0.0
|
1.0
|
C2
|
A:7GU9
|
3.3
|
0.0
|
1.0
|
N3
|
A:DT10
|
3.3
|
0.0
|
1.0
|
O2
|
B:DT17
|
3.3
|
0.0
|
1.0
|
N4
|
B:DC16
|
3.4
|
0.0
|
1.0
|
C4
|
B:DT17
|
3.5
|
0.0
|
1.0
|
N2
|
A:7GU9
|
3.6
|
0.0
|
1.0
|
O2
|
A:DT10
|
3.6
|
0.0
|
1.0
|
C2
|
A:DT10
|
3.7
|
0.0
|
1.0
|
AG
|
A:AG103
|
3.7
|
0.0
|
1.0
|
N1
|
B:DT17
|
3.8
|
0.0
|
1.0
|
O4
|
B:DT17
|
4.0
|
0.0
|
1.0
|
C4
|
A:DT10
|
4.1
|
0.0
|
1.0
|
C5
|
B:DT17
|
4.2
|
0.0
|
1.0
|
C5
|
A:7GU9
|
4.3
|
0.0
|
1.0
|
C6
|
B:DT17
|
4.3
|
0.0
|
1.0
|
N1
|
B:DC16
|
4.3
|
0.0
|
1.0
|
H42
|
B:DC16
|
4.4
|
0.0
|
1.0
|
O4
|
A:DT10
|
4.4
|
0.0
|
1.0
|
HN61
|
B:7DA15
|
4.4
|
0.0
|
1.0
|
HN61
|
A:7DA8
|
4.5
|
0.0
|
1.0
|
C5
|
B:DC16
|
4.5
|
0.0
|
1.0
|
N3
|
A:7GU9
|
4.6
|
0.0
|
1.0
|
HN22
|
A:7GU9
|
4.6
|
0.0
|
1.0
|
N1
|
B:7DA15
|
4.6
|
0.0
|
1.0
|
H1'
|
B:DT17
|
4.6
|
0.0
|
1.0
|
C1'
|
B:DT17
|
4.7
|
0.0
|
1.0
|
N1
|
A:DT10
|
4.8
|
0.0
|
1.0
|
N6
|
B:7DA15
|
4.8
|
0.0
|
1.0
|
C4
|
A:7GU9
|
4.9
|
0.0
|
1.0
|
C6
|
B:7DA15
|
4.9
|
0.0
|
1.0
|
C6
|
B:DC16
|
5.0
|
0.0
|
1.0
|
|
Silver binding site 10 out
of 12 in 9gdm
Go back to
Silver Binding Sites List in 9gdm
Silver binding site 10 out
of 12 in the Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 10 of Solution Structure of A Silver Ion Mediated Dna Duplex with Universal 7-Deazapurine Substitutions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag103
b:0.0
occ:1.00
|
N1
|
A:7GU7
|
2.2
|
0.0
|
1.0
|
N3
|
B:DC18
|
2.2
|
0.0
|
1.0
|
H41
|
B:DC18
|
2.8
|
0.0
|
1.0
|
O6
|
A:7GU7
|
2.8
|
0.0
|
1.0
|
C6
|
A:7GU7
|
2.9
|
0.0
|
1.0
|
C2
|
B:DC18
|
3.0
|
0.0
|
1.0
|
O2
|
B:DC18
|
3.0
|
0.0
|
1.0
|
N1
|
A:7DA8
|
3.1
|
0.0
|
1.0
|
HN21
|
A:7GU7
|
3.1
|
0.0
|
1.0
|
C2
|
A:7DA8
|
3.2
|
0.0
|
1.0
|
C4
|
B:DC18
|
3.2
|
0.0
|
1.0
|
H2
|
A:7DA8
|
3.2
|
0.0
|
1.0
|
C6
|
B:7GU19
|
3.3
|
0.0
|
1.0
|
C2
|
A:7GU7
|
3.3
|
0.0
|
1.0
|
N1
|
B:7GU19
|
3.4
|
0.0
|
1.0
|
N4
|
B:DC18
|
3.4
|
0.0
|
1.0
|
C5
|
B:7GU19
|
3.5
|
0.0
|
1.0
|
N2
|
A:7GU7
|
3.6
|
0.0
|
1.0
|
C2
|
B:7GU19
|
3.6
|
0.0
|
1.0
|
O6
|
B:7GU19
|
3.7
|
0.0
|
1.0
|
C6
|
A:7DA8
|
3.8
|
0.0
|
1.0
|
C4
|
B:7GU19
|
3.8
|
0.0
|
1.0
|
N3
|
B:7GU19
|
3.9
|
0.0
|
1.0
|
N3
|
A:7DA8
|
3.9
|
0.0
|
1.0
|
AG
|
A:AG103
|
4.0
|
0.0
|
1.0
|
C7
|
B:7GU19
|
4.3
|
0.0
|
1.0
|
C5
|
A:7GU7
|
4.3
|
0.0
|
1.0
|
N1
|
B:DC18
|
4.4
|
0.0
|
1.0
|
H42
|
B:DC18
|
4.4
|
0.0
|
1.0
|
N2
|
B:7GU19
|
4.4
|
0.0
|
1.0
|
C5
|
A:7DA8
|
4.4
|
0.0
|
1.0
|
N6
|
A:7DA8
|
4.4
|
0.0
|
1.0
|
HN61
|
A:7DA8
|
4.4
|
0.0
|
1.0
|
AG
|
A:AG104
|
4.4
|
0.0
|
1.0
|
C4
|
A:7DA8
|
4.4
|
0.0
|
1.0
|
C5
|
B:DC18
|
4.5
|
0.0
|
1.0
|
HN22
|
A:7GU7
|
4.6
|
0.0
|
1.0
|
N3
|
A:7GU7
|
4.6
|
0.0
|
1.0
|
N9
|
B:7GU19
|
4.6
|
0.0
|
1.0
|
H41
|
A:DC6
|
4.7
|
0.0
|
1.0
|
H7
|
B:7GU19
|
4.7
|
0.0
|
1.0
|
HN21
|
B:7GU19
|
4.9
|
0.0
|
1.0
|
C8
|
B:7GU19
|
4.9
|
0.0
|
1.0
|
C4
|
A:7GU7
|
5.0
|
0.0
|
1.0
|
C6
|
B:DC18
|
5.0
|
0.0
|
1.0
|
|
Reference:
U.Javornik,
A.Perez-Romero,
C.Lopez-Chamorro,
R.M.Smith,
J.A.Dobado,
O.Palacios,
M.K.Bera,
M.Nyman,
J.Plavec,
M.A.Galindo.
Unveiling the Solution Structure of A Dna Duplex with Continuous Silver-Modified Watson-Crick Base Pairs. Nat Commun V. 15 7763 2024.
ISSN: ESSN 2041-1723
PubMed: 39237564
DOI: 10.1038/S41467-024-51876-8
Page generated: Sat Sep 28 08:33:05 2024
|