Iridium in PDB 4gxy: Rna Structure

The structure of Rna Structure, PDB code: 4gxy was solved by A.Serganov, A.Peselis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.35 / 3.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.633, 96.633, 132.684, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25

The structure of Rna Structure also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Iridium atom in the Rna Structure (pdb code 4gxy). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 7 binding sites of Iridium where determined in the Rna Structure, PDB code: 4gxy:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7;

Iridium binding site 1 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir303 b:1.0 occ:0.50 IR A:IRI303 0.0 1.0 0.5 N3 A:IRI303 2.0 0.5 0.5 N6 A:IRI303 2.0 0.2 0.5 N4 A:IRI303 2.0 0.4 0.5 N2 A:IRI303 2.0 0.7 0.5 N1 A:IRI303 2.0 0.1 0.5 N5 A:IRI303 2.0 0.0 0.5 OP1 A:A38 3.7 97.3 1.0 OP2 A:A38 4.1 0.4 1.0 OP1 A:A39 4.2 97.1 1.0 P A:A38 4.2 99.7 1.0 O4 A:U34 4.3 0.7 1.0 O4 A:U35 4.3 0.1 1.0 O5' A:A38 4.6 0.9 1.0 O6 A:G33 4.7 0.4 1.0

Iridium binding site 2 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir304 b:0.9 occ:0.37 IR A:IRI304 0.0 0.9 0.4 N4 A:IRI304 2.0 72.8 0.4 N3 A:IRI304 2.0 75.0 0.4 N1 A:IRI304 2.0 82.7 0.4 N6 A:IRI304 2.0 79.3 0.4 N5 A:IRI304 2.0 79.0 0.4 N2 A:IRI304 2.0 74.9 0.4 OP1 A:C67 3.6 75.5 1.0 OP1 A:G64 4.1 60.5 1.0 OP2 A:G65 4.1 75.3 1.0 OP1 A:G65 4.3 77.0 1.0 P A:G65 4.8 65.6 1.0 P A:C67 4.9 74.3 1.0

Iridium binding site 3 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir305 b:0.5 occ:0.38 IR A:IRI305 0.0 0.5 0.4 N4 A:IRI305 2.0 97.1 0.4 N5 A:IRI305 2.0 92.3 0.4 N3 A:IRI305 2.0 94.5 0.4 N1 A:IRI305 2.0 96.5 0.4 N2 A:IRI305 2.0 89.4 0.4 N6 A:IRI305 2.0 91.7 0.4 OP1 A:U100 3.8 87.5 1.0 OP1 A:G101 4.7 82.0 1.0 O5' A:U100 4.8 82.6 1.0 P A:U100 4.9 76.4 1.0

Iridium binding site 4 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir306 b:96.0 occ:0.80 IR A:IRI306 0.0 96.0 0.8 N6 A:IRI306 2.0 85.1 0.8 N2 A:IRI306 2.0 79.4 0.8 N4 A:IRI306 2.0 74.3 0.8 N5 A:IRI306 2.0 78.5 0.8 N3 A:IRI306 2.0 69.4 0.8 N1 A:IRI306 2.0 63.6 0.8 O6 A:G65 3.9 62.1 1.0 OP2 A:C68 4.1 72.1 1.0 OP2 A:C69 4.1 72.5 1.0 N7 A:G65 4.4 59.7 1.0 C6 A:G65 4.7 55.4 1.0 C5 A:G65 4.9 54.3 1.0 P A:C68 5.0 63.5 1.0

Iridium binding site 5 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir307 b:0.7 occ:0.39 IR A:IRI307 0.0 0.7 0.4 N5 A:IRI307 2.0 82.8 0.4 N1 A:IRI307 2.0 81.5 0.4 N4 A:IRI307 2.0 80.7 0.4 N3 A:IRI307 2.0 89.4 0.4 N2 A:IRI307 2.0 89.4 0.4 N6 A:IRI307 2.0 90.6 0.4 OP1 A:A73 3.6 68.8 1.0 OP2 A:G151 4.1 69.0 1.0 OP1 A:C72 4.2 82.5 1.0 OP1 A:A150 4.4 80.9 1.0 O5' A:C72 4.7 62.0 1.0 P A:C72 4.9 76.4 1.0

Iridium binding site 6 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir308 b:95.1 occ:0.52 IR A:IRI308 0.0 95.1 0.5 N2 A:IRI308 2.0 79.7 0.5 N1 A:IRI308 2.0 89.2 0.5 N3 A:IRI308 2.0 73.5 0.5 N4 A:IRI308 2.0 81.7 0.5 N6 A:IRI308 2.0 75.0 0.5 N5 A:IRI308 2.0 75.2 0.5 OP2 A:C104 4.1 74.7 1.0 OP2 A:G123 4.2 66.9 1.0 OP1 A:G103 4.3 94.6 1.0 N7 A:G123 4.4 57.7 1.0 OP2 A:G122 4.5 57.9 1.0

Iridium binding site 7 out of 7 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir309 b:0.0 occ:0.50 IR A:IRI309 0.0 0.0 0.5 N3 A:IRI309 2.0 94.3 0.5 N4 A:IRI309 2.0 84.2 0.5 N2 A:IRI309 2.0 0.1 0.5 N6 A:IRI309 2.0 89.9 0.5 N5 A:IRI309 2.0 0.8 0.5 N1 A:IRI309 2.0 98.8 0.5 O6 A:G42 3.9 66.8 1.0 O6 A:G41 4.2 74.5 1.0 OP1 A:A157 4.6 62.8 1.0

A.Peselis, A.Serganov. Structural Insights Into Ligand Binding and Gene Expression Control By An Adenosylcobalamin Riboswitch. Nat.Struct.Mol.Biol. V. 19 1182 2012.
ISSN: ISSN 1545-9993
PubMed: 23064646
DOI: 10.1038/NSMB.2405