Iridium in PDB 3f2t: Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak., PDB code: 3f2t was solved by A.A.Serganov, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.493, 71.493, 138.718, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25.2

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Potassium	(K)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iridium atom in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. (pdb code 3f2t). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 12 binding sites of Iridium where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak., PDB code: 3f2t:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir401 b:0.8 occ:0.60 IR X:IRI401 0.0 0.8 0.6 N3 X:IRI401 2.0 0.9 0.4 N3 X:IRI401 2.0 0.6 0.6 N5 X:IRI401 2.0 0.7 0.6 N4 X:IRI401 2.0 0.4 0.6 N2 X:IRI401 2.0 0.6 0.6 N1 X:IRI401 2.0 0.6 0.6 N6 X:IRI401 2.0 0.9 0.6 N4 X:IRI401 2.9 0.5 0.4 N5 X:IRI401 3.1 0.5 0.4 IR X:IRI401 3.2 1.0 0.4 N7 X:G97 4.2 0.8 1.0 O6 X:G98 4.3 0.8 1.0 O6 X:G97 4.3 0.5 1.0 N6 X:IRI401 4.4 0.4 0.4 N2 X:IRI401 4.5 0.7 0.4 O2 X:FMN200 4.6 78.6 1.0 C2 X:A99 4.7 0.6 1.0 C5 X:G97 4.8 0.1 1.0 C6 X:G97 4.8 0.9 1.0 N1 X:IRI401 5.0 0.2 0.4

Iridium binding site 2 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir401 b:1.0 occ:0.40 IR X:IRI401 0.0 1.0 0.4 N6 X:IRI401 2.0 0.4 0.4 N4 X:IRI401 2.0 0.5 0.4 N5 X:IRI401 2.0 0.5 0.4 N1 X:IRI401 2.0 0.2 0.4 N2 X:IRI401 2.0 0.7 0.4 N3 X:IRI401 2.0 0.9 0.4 N6 X:IRI401 2.0 0.9 0.6 N1 X:IRI401 2.9 0.6 0.6 N2 X:IRI401 3.1 0.6 0.6 IR X:IRI401 3.2 0.8 0.6 O6 X:G12 4.0 0.6 1.0 OP2 X:C95 4.3 0.3 1.0 N4 X:IRI401 4.4 0.4 0.6 N3 X:IRI401 4.5 0.6 0.6 N5 X:IRI401 5.0 0.7 0.6 O2 X:FMN200 5.0 78.6 1.0

Iridium binding site 3 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir402 b:0.2 occ:0.60 IR X:IRI402 0.0 0.2 0.6 N3 X:IRI402 2.0 0.1 0.6 N2 X:IRI402 2.0 0.2 0.6 N4 X:IRI402 2.0 0.1 0.6 N5 X:IRI402 2.0 1.0 0.6 N6 X:IRI402 2.0 0.0 0.6 N1 X:IRI402 2.0 0.1 0.6 OP1 X:U39 3.9 1.0 1.0 OP2 X:U37 4.0 0.7 1.0 OP1 X:U37 4.6 0.6 1.0 P X:U37 4.6 0.4 1.0 O5' X:A38 4.6 0.5 1.0 O5' X:U37 4.7 0.1 1.0

Iridium binding site 4 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir403 b:0.3 occ:0.60 IR X:IRI403 0.0 0.3 0.6 N2 X:IRI403 2.0 0.1 0.6 N6 X:IRI403 2.0 0.9 0.6 N5 X:IRI403 2.0 0.9 0.6 N4 X:IRI403 2.0 0.1 0.6 N1 X:IRI403 2.0 0.8 0.6 N3 X:IRI403 2.0 0.8 0.6 OP2 X:A102 3.9 0.4 1.0 O6 X:G9 3.9 0.5 1.0 N7 X:G9 4.3 0.4 1.0 OP2 X:G101 4.5 0.9 1.0 C6 X:G9 4.6 0.1 1.0 O6 X:G103 4.7 0.6 1.0 OP1 X:G101 4.8 0.3 1.0 C5 X:G9 4.8 0.1 1.0

Iridium binding site 5 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir404 b:0.9 occ:0.70 IR X:IRI404 0.0 0.9 0.7 N5 X:IRI404 2.0 0.8 0.7 N2 X:IRI404 2.0 0.8 0.7 N4 X:IRI404 2.0 1.0 0.7 N6 X:IRI404 2.0 0.5 0.7 N3 X:IRI404 2.0 0.6 0.7 N1 X:IRI404 2.0 0.3 0.7 N7 X:G16 3.9 0.5 1.0 O6 X:G16 4.4 0.8 1.0 C5 X:G16 4.7 0.1 1.0 C8 X:G16 4.7 0.6 1.0 C6 X:G16 4.9 0.5 1.0

Iridium binding site 6 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir405 b:0.6 occ:0.60 IR X:IRI405 0.0 0.6 0.6 N3 X:IRI405 2.0 0.6 0.6 N5 X:IRI405 2.0 0.2 0.6 N2 X:IRI405 2.0 0.6 0.6 N4 X:IRI405 2.0 0.6 0.6 N6 X:IRI405 2.0 0.3 0.6 N1 X:IRI405 2.0 0.5 0.6 O4 X:U110 3.9 0.2 1.0 O4 X:U111 4.2 0.3 1.0 O6 X:GTP1 4.5 0.1 1.0 O6 X:G2 4.6 0.3 1.0

Iridium binding site 7 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir406 b:0.9 occ:0.50 IR X:IRI406 0.0 0.9 0.5 N2 X:IRI406 2.0 0.9 0.5 N4 X:IRI406 2.0 0.9 0.5 N6 X:IRI406 2.0 0.7 0.5 N1 X:IRI406 2.0 0.5 0.5 N3 X:IRI406 2.0 0.5 0.5 N5 X:IRI406 2.0 0.6 0.5 OP2 X:C58 3.7 0.3 1.0 OP2 X:G47 4.2 1.0 1.0 OP1 X:C46 4.3 0.5 1.0 OP1 X:G47 4.4 0.7 1.0 O4 X:U61 4.5 0.6 1.0 P X:C58 4.7 0.5 1.0 P X:G47 4.7 0.8 1.0 O5' X:C58 4.9 0.5 1.0

Iridium binding site 8 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir407 b:0.2 occ:0.50 IR X:IRI407 0.0 0.2 0.5 N3 X:IRI407 2.0 0.5 0.5 N6 X:IRI407 2.0 0.9 0.5 N5 X:IRI407 2.0 0.0 0.5 N4 X:IRI407 2.0 0.7 0.5 N2 X:IRI407 2.0 0.9 0.5 N1 X:IRI407 2.0 0.7 0.5 OP2 X:C76 4.2 98.4 1.0 O4 X:U64 4.2 0.8 1.0 O4 X:U42 4.8 0.6 1.0

Iridium binding site 9 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir408 b:0.4 occ:0.50 IR X:IRI408 0.0 0.4 0.5 N2 X:IRI408 2.0 0.2 0.5 N3 X:IRI408 2.0 0.2 0.5 N5 X:IRI408 2.0 0.1 0.5 N1 X:IRI408 2.0 0.2 0.5 N6 X:IRI408 2.0 0.2 0.5 N4 X:IRI408 2.0 0.2 0.5 OP2 X:A49 4.3 97.6 1.0 O4 X:U52 4.8 88.8 1.0 N7 X:A50 4.8 75.3 1.0 OP2 X:A50 4.9 79.8 1.0 O6 X:G51 5.0 80.0 1.0

Iridium binding site 10 out of 12 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak.


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 the Fmn Riboswitch Bound to Fmn, Iridium Hexamine Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Ir409 b:0.9 occ:0.30 IR X:IRI409 0.0 0.9 0.3 N6 X:IRI409 2.0 0.7 0.3 N4 X:IRI409 2.0 0.6 0.3 N2 X:IRI409 2.0 0.6 0.3 N5 X:IRI409 2.0 0.7 0.3 N3 X:IRI409 2.0 0.6 0.3 N1 X:IRI409 2.0 0.7 0.3 OP1 X:G33 3.5 0.2 1.0 OP1 X:A40 4.4 99.7 1.0 P X:G33 4.6 0.4 1.0 OP2 X:U34 4.7 0.3 1.0 OP2 X:G33 4.8 0.5 1.0

A.Serganov, L.Huang, D.J.Patel. Coenzyme Recognition and Gene Regulation By A Flavin Mononucleotide Riboswitch. Nature V. 458 233 2009.
ISSN: ISSN 0028-0836
PubMed: 19169240
DOI: 10.1038/NATURE07642