Iridium in PDB 3owz: Crystal Structure of Glycine Riboswitch, Soaked in Iridium

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

The structure of Crystal Structure of Glycine Riboswitch, Soaked in Iridium also contains other interesting chemical elements:

Magnesium

(Mg)

16 atoms

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 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 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 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 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 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 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 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 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 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 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

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