Silver in PDB 7ecl: Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Protein crystallography data
The structure of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair, PDB code: 7ecl
was solved by
J.Kondo,
Y.Uchida,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.11 /
3.01
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.252,
43.252,
378.967,
90,
90,
120
|
R / Rfree (%)
|
21.8 /
29.3
|
Other elements in 7ecl:
The structure of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair 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 Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
(pdb code 7ecl). This binding sites where shown within
5.0 Angstroms radius around Silver atom.
In total 23 binding sites of Silver where determined in the
Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair, PDB code: 7ecl:
Jump to Silver binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Silver binding site 1 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 1 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 1 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ag101
b:72.7
occ:0.76
|
N1
|
B:A9
|
1.8
|
45.2
|
1.0
|
N3
|
A:C4
|
2.2
|
55.4
|
1.0
|
N6
|
A:A3
|
2.5
|
41.0
|
1.0
|
C6
|
B:A9
|
2.7
|
48.2
|
1.0
|
N6
|
B:A9
|
2.8
|
50.4
|
1.0
|
C2
|
B:A9
|
2.8
|
44.8
|
1.0
|
N4
|
A:C4
|
2.8
|
56.2
|
1.0
|
C4
|
A:C4
|
2.9
|
54.5
|
1.0
|
C6
|
A:A3
|
3.1
|
47.4
|
1.0
|
O4
|
A:U5
|
3.1
|
47.2
|
1.0
|
C2
|
A:C4
|
3.3
|
55.5
|
1.0
|
C4
|
A:U5
|
3.5
|
53.8
|
1.0
|
O2
|
A:C4
|
3.5
|
54.1
|
1.0
|
O4
|
B:U10
|
3.5
|
50.2
|
1.0
|
N1
|
A:A3
|
3.5
|
46.5
|
1.0
|
N6
|
B:A8
|
4.0
|
49.0
|
1.0
|
C5
|
B:A9
|
4.0
|
45.4
|
1.0
|
C5
|
A:A3
|
4.0
|
51.9
|
1.0
|
C5
|
A:U5
|
4.0
|
54.3
|
1.0
|
C4
|
B:U10
|
4.1
|
48.8
|
1.0
|
N3
|
B:A9
|
4.1
|
47.4
|
1.0
|
N3
|
A:U5
|
4.2
|
50.5
|
1.0
|
N3
|
B:U10
|
4.2
|
48.1
|
1.0
|
C5
|
A:C4
|
4.3
|
55.2
|
1.0
|
N1
|
B:A8
|
4.4
|
44.3
|
1.0
|
C4
|
B:A9
|
4.4
|
46.4
|
1.0
|
N1
|
A:C4
|
4.5
|
54.0
|
1.0
|
C6
|
B:A8
|
4.5
|
47.9
|
1.0
|
N7
|
A:A3
|
4.6
|
52.0
|
1.0
|
C2
|
A:A3
|
4.6
|
51.2
|
1.0
|
C6
|
A:C4
|
4.9
|
54.4
|
1.0
|
C6
|
A:U5
|
4.9
|
54.2
|
1.0
|
C4
|
A:A3
|
5.0
|
50.4
|
1.0
|
|
Silver binding site 2 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 2 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 2 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag101
b:69.8
occ:1.00
|
N3
|
B:C4
|
2.0
|
55.1
|
1.0
|
N1
|
A:A9
|
2.0
|
53.1
|
1.0
|
C4
|
B:C4
|
2.7
|
62.6
|
1.0
|
N4
|
B:C4
|
2.7
|
58.8
|
1.0
|
N3
|
B:U5
|
2.8
|
48.7
|
1.0
|
C6
|
A:A9
|
2.9
|
52.8
|
1.0
|
C2
|
A:A9
|
2.9
|
49.9
|
1.0
|
C2
|
B:C4
|
3.0
|
60.3
|
1.0
|
N6
|
A:A9
|
3.0
|
58.2
|
1.0
|
AG
|
B:AG102
|
3.1
|
72.5
|
1.0
|
AG
|
B:AG103
|
3.1
|
77.1
|
0.6
|
O2
|
B:C4
|
3.2
|
62.6
|
1.0
|
C2
|
B:U5
|
3.3
|
55.0
|
1.0
|
C4
|
B:U5
|
3.4
|
59.6
|
1.0
|
O2
|
B:U5
|
3.5
|
54.2
|
1.0
|
O4
|
B:U5
|
3.7
|
68.2
|
1.0
|
O4
|
A:U10
|
3.9
|
50.1
|
1.0
|
C5
|
B:C4
|
4.1
|
66.2
|
1.0
|
N1
|
B:U5
|
4.1
|
63.8
|
1.0
|
C5
|
A:A9
|
4.1
|
52.9
|
1.0
|
N3
|
A:A9
|
4.2
|
43.5
|
1.0
|
N1
|
B:C4
|
4.2
|
65.5
|
1.0
|
C5
|
B:U5
|
4.2
|
66.5
|
1.0
|
N6
|
B:A3
|
4.3
|
61.8
|
1.0
|
C4
|
A:U10
|
4.4
|
51.0
|
1.0
|
C6
|
B:U5
|
4.5
|
65.9
|
1.0
|
C4
|
A:A9
|
4.6
|
50.0
|
1.0
|
N1
|
A:A8
|
4.6
|
47.8
|
1.0
|
N3
|
A:U10
|
4.6
|
54.8
|
1.0
|
C6
|
B:C4
|
4.7
|
66.8
|
1.0
|
C6
|
B:A3
|
4.8
|
58.7
|
1.0
|
N1
|
B:A3
|
4.9
|
55.3
|
1.0
|
|
Silver binding site 3 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 3 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 3 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag102
b:72.5
occ:0.99
|
N3
|
B:U5
|
2.1
|
48.7
|
1.0
|
N1
|
A:A8
|
2.1
|
47.8
|
1.0
|
O2
|
B:U5
|
2.7
|
54.2
|
1.0
|
C2
|
B:U5
|
2.8
|
55.0
|
1.0
|
C2
|
A:A8
|
3.0
|
48.9
|
1.0
|
AG
|
B:AG101
|
3.1
|
69.8
|
1.0
|
C6
|
A:A8
|
3.1
|
50.9
|
1.0
|
N6
|
A:A8
|
3.2
|
63.0
|
1.0
|
C4
|
B:U5
|
3.2
|
59.6
|
1.0
|
O4
|
B:U5
|
3.4
|
68.2
|
1.0
|
N4
|
B:CBR6
|
3.5
|
58.6
|
1.0
|
N1
|
A:A9
|
3.5
|
53.1
|
1.0
|
C6
|
A:A9
|
3.5
|
52.8
|
1.0
|
C4
|
B:CBR6
|
3.6
|
53.0
|
1.0
|
N6
|
A:A9
|
3.7
|
58.2
|
1.0
|
N3
|
B:CBR6
|
3.9
|
52.8
|
1.0
|
C5
|
B:CBR6
|
4.0
|
53.1
|
1.0
|
C2
|
A:A9
|
4.1
|
49.9
|
1.0
|
N1
|
B:U5
|
4.1
|
63.8
|
1.0
|
C5
|
A:A9
|
4.2
|
52.9
|
1.0
|
N3
|
A:A8
|
4.3
|
46.4
|
1.0
|
C5
|
A:A8
|
4.4
|
48.4
|
1.0
|
C5
|
B:U5
|
4.4
|
66.5
|
1.0
|
BR
|
B:CBR6
|
4.6
|
80.2
|
1.0
|
C4
|
A:A9
|
4.6
|
50.0
|
1.0
|
N4
|
B:C4
|
4.7
|
58.8
|
1.0
|
N3
|
B:C4
|
4.7
|
55.1
|
1.0
|
C2
|
B:CBR6
|
4.7
|
50.6
|
1.0
|
C6
|
B:CBR6
|
4.7
|
54.5
|
1.0
|
O6
|
A:G7
|
4.7
|
52.6
|
1.0
|
N3
|
A:A9
|
4.7
|
43.5
|
1.0
|
C6
|
B:U5
|
4.8
|
65.9
|
1.0
|
C4
|
A:A8
|
4.8
|
48.0
|
1.0
|
N7
|
A:A9
|
5.0
|
53.2
|
1.0
|
N1
|
B:CBR6
|
5.0
|
54.7
|
1.0
|
|
Silver binding site 4 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 4 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 4 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ag103
b:77.1
occ:0.61
|
N1
|
B:A3
|
2.2
|
55.3
|
1.0
|
O4
|
A:U10
|
2.2
|
50.1
|
1.0
|
N6
|
B:A3
|
2.5
|
61.8
|
1.0
|
N3
|
A:U10
|
2.6
|
54.8
|
1.0
|
C6
|
B:A3
|
2.6
|
58.7
|
1.0
|
C4
|
A:U10
|
2.8
|
51.0
|
1.0
|
N3
|
B:C4
|
3.0
|
55.1
|
1.0
|
AG
|
B:AG101
|
3.1
|
69.8
|
1.0
|
C2
|
B:A3
|
3.3
|
57.0
|
1.0
|
N1
|
A:A9
|
3.3
|
53.1
|
1.0
|
C2
|
B:C4
|
3.4
|
60.3
|
1.0
|
O2
|
B:C4
|
3.4
|
62.6
|
1.0
|
C4
|
B:C4
|
3.7
|
62.6
|
1.0
|
C2
|
A:U10
|
3.8
|
49.4
|
1.0
|
C5
|
B:A3
|
3.9
|
60.5
|
1.0
|
C2
|
A:A9
|
3.9
|
49.9
|
1.0
|
N4
|
B:C4
|
4.0
|
58.8
|
1.0
|
C6
|
A:A9
|
4.1
|
52.8
|
1.0
|
N6
|
A:A9
|
4.1
|
58.2
|
1.0
|
N4
|
A:C11
|
4.1
|
50.7
|
1.0
|
C4
|
A:C11
|
4.2
|
53.6
|
1.0
|
C5
|
A:U10
|
4.2
|
50.0
|
1.0
|
N3
|
A:C11
|
4.2
|
56.0
|
1.0
|
O2
|
A:U10
|
4.2
|
41.7
|
1.0
|
N1
|
B:C4
|
4.4
|
65.5
|
1.0
|
N3
|
B:A3
|
4.4
|
63.8
|
1.0
|
O6
|
B:G2
|
4.5
|
58.3
|
1.0
|
C4
|
B:A3
|
4.6
|
64.0
|
1.0
|
C5
|
B:C4
|
4.7
|
66.2
|
1.0
|
C5
|
A:C11
|
4.8
|
51.6
|
1.0
|
C2
|
A:C11
|
4.8
|
49.3
|
1.0
|
N1
|
A:U10
|
4.9
|
45.3
|
1.0
|
C6
|
B:C4
|
5.0
|
66.8
|
1.0
|
N1
|
B:G2
|
5.0
|
54.5
|
1.0
|
C6
|
A:U10
|
5.0
|
45.1
|
1.0
|
|
Silver binding site 5 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 5 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 5 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ag101
b:69.0
occ:0.73
|
N3
|
D:U5
|
2.2
|
46.0
|
1.0
|
O4
|
D:U5
|
2.6
|
52.6
|
1.0
|
N1
|
C:A8
|
2.6
|
48.0
|
1.0
|
N6
|
C:A8
|
2.7
|
43.7
|
1.0
|
C4
|
D:U5
|
2.8
|
46.3
|
1.0
|
N1
|
C:A9
|
3.0
|
39.3
|
1.0
|
C6
|
C:A9
|
3.1
|
35.1
|
1.0
|
C6
|
C:A8
|
3.1
|
46.9
|
1.0
|
N4
|
D:CBR6
|
3.2
|
56.8
|
1.0
|
C2
|
C:A9
|
3.2
|
45.8
|
1.0
|
C2
|
D:U5
|
3.3
|
50.3
|
1.0
|
C4
|
D:CBR6
|
3.4
|
54.1
|
1.0
|
C5
|
C:A9
|
3.5
|
44.5
|
1.0
|
N3
|
D:CBR6
|
3.6
|
56.1
|
1.0
|
O2
|
D:U5
|
3.6
|
47.0
|
1.0
|
N6
|
C:A9
|
3.6
|
35.7
|
1.0
|
N3
|
C:A9
|
3.6
|
42.9
|
1.0
|
C4
|
C:A9
|
3.6
|
44.0
|
1.0
|
C2
|
C:A8
|
3.8
|
49.7
|
1.0
|
C5
|
D:CBR6
|
4.1
|
50.9
|
1.0
|
C5
|
D:U5
|
4.2
|
46.3
|
1.0
|
AG
|
D:AG101
|
4.3
|
52.4
|
1.0
|
N7
|
C:A9
|
4.3
|
49.2
|
1.0
|
N1
|
C:G7
|
4.4
|
56.0
|
1.0
|
C2
|
D:CBR6
|
4.4
|
55.9
|
1.0
|
O6
|
C:G7
|
4.5
|
59.9
|
1.0
|
N1
|
D:U5
|
4.5
|
56.3
|
1.0
|
C5
|
C:A8
|
4.5
|
52.3
|
1.0
|
N9
|
C:A9
|
4.6
|
46.9
|
1.0
|
C6
|
D:U5
|
4.8
|
53.9
|
1.0
|
C6
|
C:G7
|
4.8
|
58.9
|
1.0
|
C6
|
D:CBR6
|
4.9
|
56.7
|
1.0
|
C8
|
C:A9
|
4.9
|
47.4
|
1.0
|
BR
|
D:CBR6
|
4.9
|
77.1
|
1.0
|
|
Silver binding site 6 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 6 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 6 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ag102
b:94.4
occ:0.67
|
N1
|
D:A9
|
2.0
|
74.5
|
1.0
|
N3
|
C:C4
|
2.1
|
70.5
|
1.0
|
N6
|
D:A9
|
2.4
|
73.2
|
1.0
|
C6
|
D:A9
|
2.5
|
73.5
|
1.0
|
N4
|
C:C4
|
2.7
|
67.3
|
1.0
|
C4
|
C:C4
|
2.8
|
66.2
|
1.0
|
C2
|
D:A9
|
3.1
|
75.3
|
1.0
|
N3
|
D:U10
|
3.2
|
60.1
|
1.0
|
C2
|
C:C4
|
3.2
|
66.7
|
1.0
|
AG
|
D:AG103
|
3.3
|
102.0
|
0.7
|
C4
|
C:U5
|
3.3
|
61.5
|
1.0
|
N3
|
C:U5
|
3.4
|
64.5
|
1.0
|
O4
|
C:U5
|
3.4
|
66.1
|
1.0
|
AG
|
D:AG102
|
3.4
|
68.3
|
0.6
|
O2
|
C:C4
|
3.5
|
63.6
|
1.0
|
O4
|
D:U10
|
3.5
|
66.0
|
1.0
|
C4
|
D:U10
|
3.5
|
60.0
|
1.0
|
C5
|
C:U5
|
3.8
|
62.5
|
1.0
|
C5
|
D:A9
|
3.9
|
71.3
|
1.0
|
C2
|
D:U10
|
3.9
|
65.8
|
1.0
|
C2
|
C:U5
|
4.0
|
71.1
|
1.0
|
O2
|
D:U10
|
4.2
|
65.1
|
1.0
|
C5
|
C:C4
|
4.2
|
64.3
|
1.0
|
N3
|
D:A9
|
4.3
|
72.8
|
1.0
|
N1
|
C:A3
|
4.4
|
59.8
|
1.0
|
C6
|
C:U5
|
4.4
|
61.5
|
1.0
|
N1
|
C:U5
|
4.5
|
67.9
|
1.0
|
N1
|
C:C4
|
4.5
|
61.9
|
1.0
|
C4
|
D:A9
|
4.5
|
72.5
|
1.0
|
C5
|
D:U10
|
4.6
|
66.6
|
1.0
|
N6
|
D:A8
|
4.6
|
66.6
|
1.0
|
O2
|
C:U5
|
4.7
|
70.9
|
1.0
|
N1
|
D:A8
|
4.8
|
69.1
|
1.0
|
N1
|
D:U10
|
4.8
|
68.1
|
1.0
|
C6
|
C:C4
|
4.9
|
65.1
|
1.0
|
C2
|
C:A3
|
4.9
|
60.5
|
1.0
|
|
Silver binding site 7 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 7 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 7 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ag101
b:52.4
occ:1.00
|
N3
|
D:C4
|
2.1
|
39.4
|
1.0
|
N1
|
C:A9
|
2.1
|
39.3
|
1.0
|
N6
|
C:A9
|
2.4
|
35.7
|
1.0
|
O2
|
D:C4
|
2.6
|
43.8
|
1.0
|
C6
|
C:A9
|
2.7
|
35.1
|
1.0
|
C2
|
D:C4
|
2.7
|
39.1
|
1.0
|
O4
|
D:U5
|
2.8
|
52.6
|
1.0
|
C4
|
D:U5
|
2.9
|
46.3
|
1.0
|
O4
|
C:U10
|
2.9
|
36.6
|
1.0
|
C5
|
D:U5
|
3.2
|
46.3
|
1.0
|
C4
|
D:C4
|
3.2
|
49.3
|
1.0
|
N6
|
D:A3
|
3.2
|
41.5
|
1.0
|
C2
|
C:A9
|
3.2
|
45.8
|
1.0
|
C4
|
C:U10
|
3.4
|
41.2
|
1.0
|
N4
|
D:C4
|
3.5
|
54.7
|
1.0
|
N3
|
D:U5
|
3.7
|
46.0
|
1.0
|
N3
|
C:U10
|
3.7
|
40.7
|
1.0
|
C6
|
D:A3
|
3.8
|
46.4
|
1.0
|
C6
|
D:U5
|
4.0
|
53.9
|
1.0
|
N1
|
D:A3
|
4.0
|
48.6
|
1.0
|
C5
|
C:A9
|
4.0
|
44.5
|
1.0
|
N1
|
D:C4
|
4.1
|
50.8
|
1.0
|
C5
|
C:U10
|
4.2
|
43.1
|
1.0
|
AG
|
C:AG101
|
4.3
|
69.0
|
0.7
|
N3
|
C:A9
|
4.5
|
42.9
|
1.0
|
C2
|
D:U5
|
4.5
|
50.3
|
1.0
|
C5
|
D:C4
|
4.5
|
49.3
|
1.0
|
N1
|
D:U5
|
4.6
|
56.3
|
1.0
|
C4
|
C:A9
|
4.7
|
44.0
|
1.0
|
C2
|
C:U10
|
4.7
|
40.9
|
1.0
|
C6
|
D:C4
|
4.8
|
51.0
|
1.0
|
C5
|
D:A3
|
4.8
|
43.4
|
1.0
|
|
Silver binding site 8 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 8 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 8 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ag102
b:68.3
occ:0.62
|
N3
|
D:U10
|
2.1
|
60.1
|
1.0
|
N1
|
C:A3
|
2.1
|
59.8
|
1.0
|
C2
|
C:A3
|
2.4
|
60.5
|
1.0
|
O4
|
D:U10
|
2.4
|
66.0
|
1.0
|
C4
|
D:U10
|
2.6
|
60.0
|
1.0
|
C4
|
D:C11
|
3.0
|
54.1
|
1.0
|
N4
|
D:C11
|
3.0
|
50.9
|
1.0
|
C2
|
D:U10
|
3.2
|
65.8
|
1.0
|
N3
|
D:C11
|
3.3
|
49.8
|
1.0
|
O6
|
C:G2
|
3.3
|
56.4
|
1.0
|
C6
|
C:A3
|
3.4
|
67.7
|
1.0
|
N3
|
C:C4
|
3.4
|
70.5
|
1.0
|
AG
|
C:AG102
|
3.4
|
94.4
|
0.7
|
O2
|
D:U10
|
3.5
|
65.1
|
1.0
|
C5
|
D:C11
|
3.6
|
53.1
|
1.0
|
C4
|
C:C4
|
3.6
|
66.2
|
1.0
|
N3
|
C:A3
|
3.7
|
65.6
|
1.0
|
N4
|
C:C4
|
3.7
|
67.3
|
1.0
|
C5
|
D:U10
|
3.9
|
66.6
|
1.0
|
N6
|
C:A3
|
4.0
|
77.6
|
1.0
|
C2
|
D:C11
|
4.0
|
47.4
|
1.0
|
C2
|
C:C4
|
4.1
|
66.7
|
1.0
|
C6
|
C:G2
|
4.1
|
54.8
|
1.0
|
C6
|
D:C11
|
4.2
|
52.2
|
1.0
|
N1
|
C:G2
|
4.3
|
52.4
|
1.0
|
N1
|
D:U10
|
4.3
|
68.1
|
1.0
|
N6
|
D:A9
|
4.3
|
73.2
|
1.0
|
N1
|
D:C11
|
4.4
|
46.9
|
1.0
|
N1
|
D:A9
|
4.4
|
74.5
|
1.0
|
C5
|
C:C4
|
4.4
|
64.3
|
1.0
|
C5
|
C:A3
|
4.5
|
70.4
|
1.0
|
C4
|
C:A3
|
4.5
|
70.6
|
1.0
|
O2
|
C:C4
|
4.5
|
63.6
|
1.0
|
C6
|
D:U10
|
4.6
|
68.6
|
1.0
|
C6
|
D:A9
|
4.7
|
73.5
|
1.0
|
O2
|
D:C11
|
4.7
|
47.0
|
1.0
|
N1
|
C:C4
|
4.8
|
61.9
|
1.0
|
C6
|
C:C4
|
4.9
|
65.1
|
1.0
|
|
Silver binding site 9 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 9 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 9 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ag103
b:102.0
occ:0.68
|
N3
|
C:U5
|
2.1
|
64.5
|
1.0
|
O4
|
C:U5
|
2.2
|
66.1
|
1.0
|
N1
|
D:A8
|
2.3
|
69.1
|
1.0
|
C4
|
C:U5
|
2.5
|
61.5
|
1.0
|
N6
|
D:A8
|
2.7
|
66.6
|
1.0
|
C6
|
D:A8
|
2.9
|
66.4
|
1.0
|
AG
|
C:AG102
|
3.3
|
94.4
|
0.7
|
C2
|
C:U5
|
3.3
|
71.1
|
1.0
|
N1
|
D:A9
|
3.4
|
74.5
|
1.0
|
N6
|
D:A9
|
3.4
|
73.2
|
1.0
|
C2
|
D:A8
|
3.4
|
68.4
|
1.0
|
C6
|
D:A9
|
3.4
|
73.5
|
1.0
|
O2
|
C:U5
|
3.7
|
70.9
|
1.0
|
N4
|
C:CBR6
|
3.8
|
60.9
|
1.0
|
C4
|
C:CBR6
|
3.9
|
64.8
|
1.0
|
C5
|
C:U5
|
3.9
|
62.5
|
1.0
|
N3
|
C:CBR6
|
4.1
|
64.7
|
1.0
|
C2
|
D:A9
|
4.1
|
75.3
|
1.0
|
O6
|
D:G7
|
4.2
|
58.7
|
1.0
|
C5
|
D:A9
|
4.2
|
71.3
|
1.0
|
C5
|
D:A8
|
4.3
|
63.5
|
1.0
|
C5
|
C:CBR6
|
4.4
|
59.0
|
1.0
|
N1
|
C:U5
|
4.4
|
67.9
|
1.0
|
N1
|
D:G7
|
4.6
|
60.3
|
1.0
|
N4
|
C:C4
|
4.6
|
67.3
|
1.0
|
C6
|
C:U5
|
4.6
|
61.5
|
1.0
|
N3
|
D:A8
|
4.7
|
65.7
|
1.0
|
C6
|
D:G7
|
4.7
|
61.8
|
1.0
|
N3
|
C:C4
|
4.7
|
70.5
|
1.0
|
C4
|
D:A9
|
4.8
|
72.5
|
1.0
|
C2
|
C:CBR6
|
4.8
|
62.2
|
1.0
|
N3
|
D:A9
|
4.9
|
72.8
|
1.0
|
C4
|
D:A8
|
4.9
|
65.2
|
1.0
|
|
Silver binding site 10 out
of 23 in 7ecl
Go back to
Silver Binding Sites List in 7ecl
Silver binding site 10 out
of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair
Mono view
Stereo pair view
|
A full contact list of Silver with other atoms in the Ag binding
site number 10 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ag101
b:60.2
occ:0.75
|
N3
|
E:C4
|
2.1
|
45.7
|
1.0
|
N1
|
F:A9
|
2.2
|
45.7
|
1.0
|
N4
|
E:C4
|
2.6
|
58.1
|
1.0
|
N6
|
F:A9
|
2.6
|
45.3
|
1.0
|
C4
|
E:C4
|
2.7
|
50.5
|
1.0
|
C6
|
F:A9
|
2.8
|
46.3
|
1.0
|
N6
|
E:A3
|
3.0
|
46.0
|
1.0
|
C2
|
E:C4
|
3.2
|
50.6
|
1.0
|
O4
|
E:U5
|
3.2
|
43.0
|
1.0
|
O4
|
F:U10
|
3.2
|
42.1
|
1.0
|
C2
|
F:A9
|
3.4
|
46.9
|
1.0
|
C4
|
E:U5
|
3.4
|
42.0
|
1.0
|
O2
|
E:C4
|
3.5
|
49.2
|
1.0
|
C6
|
E:A3
|
3.5
|
45.4
|
1.0
|
C4
|
F:U10
|
3.7
|
43.0
|
1.0
|
N1
|
E:A3
|
3.8
|
44.0
|
1.0
|
N3
|
F:U10
|
3.9
|
40.7
|
1.0
|
C5
|
E:U5
|
3.9
|
40.8
|
1.0
|
N3
|
E:U5
|
4.0
|
39.7
|
1.0
|
N6
|
F:A8
|
4.0
|
33.8
|
1.0
|
C5
|
E:C4
|
4.1
|
55.6
|
1.0
|
C5
|
F:A9
|
4.2
|
49.2
|
1.0
|
N1
|
E:C4
|
4.4
|
55.9
|
1.0
|
C5
|
E:A3
|
4.4
|
47.9
|
1.0
|
N3
|
F:A9
|
4.6
|
50.0
|
1.0
|
C5
|
F:U10
|
4.6
|
43.9
|
1.0
|
C6
|
E:U5
|
4.7
|
39.5
|
1.0
|
C6
|
E:C4
|
4.8
|
56.1
|
1.0
|
C2
|
E:A3
|
4.8
|
46.0
|
1.0
|
C2
|
E:U5
|
4.8
|
45.4
|
1.0
|
C4
|
F:A9
|
4.9
|
47.1
|
1.0
|
C2
|
F:U10
|
4.9
|
46.7
|
1.0
|
C6
|
F:A8
|
5.0
|
37.5
|
1.0
|
|
Reference:
J.Kondo,
Y.Uchida.
Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair To Be Published.
Page generated: Wed Jul 10 08:52:17 2024
|