Iridium in PDB 4xwf: Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom

The structure of Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom, PDB code: 4xwf was solved by J.J.Trausch, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.75 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	40.160, 40.160, 234.910, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.9

The structure of Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Arsenic	(As)	1 atom

The binding sites of Iridium atom in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom (pdb code 4xwf). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 4 binding sites of Iridium where determined in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom, PDB code: 4xwf:
Jump to Iridium binding site number: 1; 2; 3; 4;

Iridium binding site 1 out of 4 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir105 b:0.7 occ:1.00 IR A:IRI105 0.0 0.7 1.0 N1 A:IRI105 2.3 77.5 1.0 N2 A:IRI105 2.3 59.7 1.0 N6 A:IRI105 2.3 65.0 1.0 N4 A:IRI105 2.3 88.8 1.0 N5 A:IRI105 2.3 91.4 1.0 N3 A:IRI105 2.3 77.3 1.0 O6 A:G8 4.3 31.3 1.0 N7 A:G8 4.4 30.5 1.0 O A:HOH299 4.4 54.7 1.0 O A:HOH273 4.4 33.9 1.0 O6 A:G37 4.6 25.9 1.0 OP2 A:U7 4.7 34.5 1.0

Iridium binding site 2 out of 4 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir106 b:0.2 occ:1.00 IR A:IRI106 0.0 0.2 1.0 N2 A:IRI106 2.2 88.6 1.0 N4 A:IRI106 2.3 68.6 1.0 N5 A:IRI106 2.3 0.6 1.0 N1 A:IRI106 2.3 62.2 1.0 N3 A:IRI106 2.3 0.9 1.0 N6 A:IRI106 2.3 64.8 1.0 O6 A:G61 4.3 33.7 1.0 O A:HOH292 4.4 54.2 1.0 O A:HOH289 4.5 46.4 1.0 O6 A:G60 4.5 18.4 1.0 N1 A:IRI107 4.6 0.7 1.0 N7 A:G60 4.8 21.2 1.0 N7 A:G61 4.9 28.8 1.0 N5 A:IRI107 4.9 61.3 1.0

Iridium binding site 3 out of 4 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir107 b:0.5 occ:1.00 IR A:IRI107 0.0 0.5 1.0 N2 A:IRI107 2.2 74.4 1.0 N4 A:IRI107 2.3 0.3 1.0 N6 A:IRI107 2.3 84.3 1.0 N1 A:IRI107 2.3 0.7 1.0 N5 A:IRI107 2.3 61.3 1.0 N3 A:IRI107 2.3 55.3 1.0 N7 A:G59 4.0 26.3 1.0 N2 A:IRI106 4.4 88.6 1.0 O6 A:G59 4.5 24.9 1.0 C5 A:G59 4.8 23.7 1.0 C8 A:G59 4.9 30.2 1.0

Iridium binding site 4 out of 4 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir108 b:0.5 occ:1.00 IR A:IRI108 0.0 0.5 1.0 N5 A:IRI108 2.3 98.5 1.0 N2 A:IRI108 2.3 0.7 1.0 N3 A:IRI108 2.3 99.5 1.0 N4 A:IRI108 2.3 77.1 1.0 N1 A:IRI108 2.3 0.1 1.0 N6 A:IRI108 2.3 99.6 1.0 OP1 A:C30 3.9 57.4 1.0 O A:HOH230 4.3 49.6 1.0 OP1 A:C10 4.5 32.1 1.0

J.J.Trausch, J.G.Marcano-Velazquez, M.M.Matyjasik, R.T.Batey. Metal Ion-Mediated Nucleobase Recognition By the Ztp Riboswitch. Chem.Biol. V. 22 829 2015.
ISSN: ISSN 1074-5521
PubMed: 26144884
DOI: 10.1016/J.CHEMBIOL.2015.06.007