Iridium in PDB 3owz: Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Protein crystallography data
The structure of Crystal Structure of Glycine Riboswitch, Soaked in Iridium, PDB code: 3owz
was solved by
L.Huang,
A.Serganov,
D.J.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.95
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.610,
82.610,
149.550,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21 /
23.4
|
Other elements in 3owz:
The structure of Crystal Structure of Glycine Riboswitch, Soaked in Iridium also contains other interesting chemical elements:
Iridium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
23;
Binding sites:
The binding sites of Iridium atom in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
(pdb code 3owz). This binding sites where shown within
5.0 Angstroms radius around Iridium atom.
In total 23 binding sites of Iridium where determined in the
Crystal Structure of Glycine Riboswitch, Soaked in Iridium, PDB code: 3owz:
Jump to Iridium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iridium binding site 1 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 1 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 1 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir201
b:37.7
occ:0.24
|
IR
|
A:IRI201
|
0.0
|
37.7
|
0.2
|
N4
|
A:IRI201
|
2.0
|
36.9
|
1.0
|
N3
|
A:IRI201
|
2.0
|
37.1
|
1.0
|
N5
|
A:IRI201
|
2.0
|
37.3
|
0.6
|
N2
|
A:IRI201
|
2.0
|
37.2
|
1.0
|
N1
|
A:IRI201
|
2.0
|
37.4
|
1.0
|
N6
|
A:IRI201
|
2.0
|
37.3
|
1.0
|
O6
|
A:G8
|
3.8
|
46.3
|
1.0
|
O4
|
A:U6
|
4.0
|
47.7
|
1.0
|
C6
|
A:G8
|
4.8
|
45.8
|
1.0
|
C4
|
A:U6
|
4.8
|
47.5
|
1.0
|
|
Iridium binding site 2 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 2 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 2 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir202
b:34.1
occ:0.12
|
IR
|
A:IRI202
|
0.0
|
34.1
|
0.1
|
N1
|
A:IRI202
|
2.0
|
33.4
|
1.0
|
N2
|
A:IRI202
|
2.0
|
33.7
|
1.0
|
N4
|
A:IRI202
|
2.0
|
33.9
|
0.5
|
N3
|
A:IRI202
|
2.0
|
33.9
|
0.5
|
N5
|
A:IRI202
|
2.0
|
33.9
|
0.8
|
N6
|
A:IRI202
|
2.0
|
33.9
|
1.0
|
OP2
|
A:G7
|
3.2
|
46.8
|
1.0
|
N3
|
A:IRI222
|
3.8
|
37.9
|
1.0
|
N5
|
A:IRI222
|
4.0
|
38.2
|
0.3
|
OP2
|
A:G8
|
4.1
|
42.0
|
1.0
|
N7
|
A:G8
|
4.1
|
45.2
|
1.0
|
P
|
A:G7
|
4.2
|
47.2
|
1.0
|
O5'
|
A:G7
|
4.2
|
46.6
|
1.0
|
O6
|
A:G80
|
4.6
|
44.3
|
1.0
|
OP1
|
A:G7
|
4.7
|
47.4
|
1.0
|
C8
|
A:G8
|
4.8
|
44.6
|
1.0
|
N2
|
A:IRI222
|
5.0
|
38.5
|
1.0
|
|
Iridium binding site 3 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 3 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 3 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir203
b:41.6
occ:0.23
|
IR
|
B:IRI203
|
0.0
|
41.6
|
0.2
|
N6
|
B:IRI203
|
2.0
|
41.5
|
1.0
|
N5
|
B:IRI203
|
2.0
|
41.3
|
1.0
|
N2
|
B:IRI203
|
2.0
|
41.7
|
1.0
|
N4
|
B:IRI203
|
2.0
|
41.4
|
1.0
|
N3
|
B:IRI203
|
2.0
|
41.3
|
1.0
|
N1
|
B:IRI203
|
2.0
|
41.4
|
0.2
|
OP2
|
B:G32
|
4.4
|
41.1
|
1.0
|
OP1
|
B:U67
|
4.4
|
43.3
|
1.0
|
OP2
|
B:C68
|
4.5
|
39.7
|
1.0
|
OP1
|
A:G10
|
4.9
|
39.5
|
1.0
|
|
Iridium binding site 4 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 4 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 4 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir204
b:35.4
occ:0.26
|
IR
|
A:IRI204
|
0.0
|
35.4
|
0.3
|
N2
|
A:IRI204
|
2.0
|
35.0
|
1.0
|
N1
|
A:IRI204
|
2.0
|
34.9
|
1.0
|
N6
|
A:IRI204
|
2.0
|
34.7
|
1.0
|
N3
|
A:IRI204
|
2.0
|
35.0
|
1.0
|
N5
|
A:IRI204
|
2.0
|
34.4
|
1.0
|
N4
|
A:IRI204
|
2.0
|
35.3
|
1.0
|
OP1
|
A:U67
|
4.3
|
44.1
|
1.0
|
OP2
|
A:G32
|
4.5
|
42.6
|
1.0
|
OP1
|
B:G10
|
4.6
|
42.3
|
1.0
|
OP2
|
A:C68
|
4.9
|
48.4
|
1.0
|
OP2
|
A:U67
|
5.0
|
44.7
|
1.0
|
|
Iridium binding site 5 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 5 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 5 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir205
b:32.6
occ:0.11
|
IR
|
A:IRI205
|
0.0
|
32.6
|
0.1
|
N3
|
A:IRI205
|
2.0
|
32.4
|
0.8
|
N2
|
A:IRI205
|
2.0
|
32.4
|
1.0
|
N5
|
A:IRI205
|
2.0
|
32.8
|
1.0
|
N6
|
A:IRI205
|
2.0
|
32.6
|
1.0
|
N4
|
A:IRI205
|
2.0
|
32.6
|
1.0
|
N1
|
A:IRI205
|
2.0
|
32.7
|
1.0
|
OP2
|
A:A64
|
4.1
|
41.9
|
1.0
|
OP2
|
A:A37
|
4.3
|
52.4
|
1.0
|
OP1
|
A:A64
|
4.3
|
42.0
|
1.0
|
N7
|
A:A37
|
4.5
|
47.7
|
1.0
|
P
|
A:A64
|
4.8
|
42.1
|
1.0
|
|
Iridium binding site 6 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 6 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 6 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir206
b:32.8
occ:0.16
|
IR
|
A:IRI206
|
0.0
|
32.8
|
0.2
|
N3
|
A:IRI206
|
2.0
|
32.3
|
1.0
|
N5
|
A:IRI206
|
2.0
|
32.8
|
1.0
|
N2
|
A:IRI206
|
2.0
|
32.5
|
1.0
|
N6
|
A:IRI206
|
2.0
|
32.6
|
1.0
|
N4
|
A:IRI206
|
2.0
|
32.5
|
1.0
|
N1
|
A:IRI206
|
2.0
|
32.6
|
0.5
|
N7
|
A:G62
|
3.7
|
45.8
|
1.0
|
OP2
|
A:G62
|
4.1
|
47.0
|
1.0
|
OP2
|
A:U61
|
4.1
|
48.1
|
1.0
|
OP2
|
A:C39
|
4.4
|
49.5
|
1.0
|
C8
|
A:G62
|
4.4
|
45.8
|
1.0
|
OP1
|
A:C39
|
4.6
|
49.6
|
1.0
|
C5
|
A:G62
|
4.8
|
45.4
|
1.0
|
O6
|
A:G62
|
5.0
|
46.1
|
1.0
|
P
|
A:C39
|
5.0
|
49.7
|
1.0
|
|
Iridium binding site 7 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 7 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 7 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir207
b:42.2
occ:0.40
|
IR
|
A:IRI207
|
0.0
|
42.2
|
0.4
|
N3
|
A:IRI207
|
2.0
|
41.4
|
1.0
|
N4
|
A:IRI207
|
2.0
|
41.2
|
1.0
|
N6
|
A:IRI207
|
2.0
|
41.8
|
0.7
|
N1
|
A:IRI207
|
2.0
|
41.4
|
1.0
|
N5
|
A:IRI207
|
2.0
|
41.4
|
1.0
|
N2
|
A:IRI207
|
2.0
|
41.6
|
1.0
|
O4
|
A:U61
|
4.1
|
46.3
|
1.0
|
OP2
|
A:A40
|
4.1
|
46.2
|
1.0
|
O6
|
A:G60
|
4.3
|
45.5
|
1.0
|
OP2
|
A:A41
|
4.4
|
42.2
|
1.0
|
N1
|
A:G62
|
4.7
|
45.3
|
1.0
|
|
Iridium binding site 8 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 8 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 8 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir208
b:41.7
occ:0.19
|
IR
|
B:IRI208
|
0.0
|
41.7
|
0.2
|
N5
|
B:IRI208
|
2.0
|
41.4
|
1.0
|
N2
|
B:IRI208
|
2.0
|
41.5
|
1.0
|
N3
|
B:IRI208
|
2.0
|
41.7
|
1.0
|
N1
|
B:IRI208
|
2.0
|
41.3
|
1.0
|
N4
|
B:IRI208
|
2.0
|
41.7
|
1.0
|
N6
|
B:IRI208
|
2.0
|
41.5
|
0.8
|
OP2
|
B:G7
|
3.6
|
44.8
|
1.0
|
N5
|
B:IRI219
|
3.7
|
37.8
|
1.0
|
N2
|
B:IRI219
|
4.0
|
38.5
|
1.0
|
N1
|
B:IRI219
|
4.0
|
38.0
|
0.4
|
OP2
|
B:G8
|
4.3
|
42.5
|
1.0
|
N7
|
B:G8
|
4.4
|
41.3
|
1.0
|
O6
|
B:G80
|
4.5
|
36.9
|
1.0
|
P
|
B:G7
|
4.6
|
45.5
|
1.0
|
IR
|
B:IRI219
|
4.7
|
38.1
|
0.1
|
O5'
|
B:G7
|
4.8
|
44.8
|
1.0
|
OP1
|
B:G7
|
5.0
|
45.7
|
1.0
|
|
Iridium binding site 9 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 9 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 9 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir209
b:41.5
occ:0.25
|
IR
|
B:IRI209
|
0.0
|
41.5
|
0.2
|
N3
|
B:IRI209
|
2.0
|
41.3
|
1.0
|
N4
|
B:IRI209
|
2.0
|
41.2
|
1.0
|
N1
|
B:IRI209
|
2.0
|
41.4
|
1.0
|
N6
|
B:IRI209
|
2.0
|
41.2
|
1.0
|
N5
|
B:IRI209
|
2.0
|
41.2
|
0.8
|
N2
|
B:IRI209
|
2.0
|
41.3
|
1.0
|
N4
|
B:IRI219
|
3.6
|
37.4
|
1.0
|
O6
|
B:G8
|
4.5
|
41.9
|
1.0
|
O4
|
B:U6
|
4.6
|
43.1
|
1.0
|
N5
|
B:IRI219
|
4.7
|
37.8
|
1.0
|
N3
|
B:IRI219
|
5.0
|
38.0
|
1.0
|
|
Iridium binding site 10 out
of 23 in 3owz
Go back to
Iridium Binding Sites List in 3owz
Iridium binding site 10 out
of 23 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 10 of Crystal Structure of Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir210
b:37.1
occ:0.06
|
IR
|
B:IRI210
|
0.0
|
37.1
|
0.1
|
N1
|
B:IRI210
|
2.0
|
37.1
|
1.0
|
N6
|
B:IRI210
|
2.0
|
37.1
|
1.0
|
N3
|
B:IRI210
|
2.0
|
36.8
|
1.0
|
N5
|
B:IRI210
|
2.0
|
37.7
|
1.0
|
N4
|
B:IRI210
|
2.0
|
37.0
|
1.0
|
N2
|
B:IRI210
|
2.0
|
37.0
|
1.0
|
O6
|
B:G1
|
3.6
|
61.9
|
1.0
|
N7
|
B:G1
|
4.6
|
61.8
|
1.0
|
C6
|
B:G1
|
4.6
|
62.1
|
1.0
|
C5
|
B:G1
|
5.0
|
61.9
|
1.0
|
|
Reference:
L.Huang,
A.Serganov,
D.J.Patel.
Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Mon Aug 12 03:21:14 2024
|