Atomistry » Iridium » PDB 5e1u-7onm » 6dlr
Atomistry »
  Iridium »
    PDB 5e1u-7onm »
      6dlr »

Iridium in PDB 6dlr: Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure

Protein crystallography data

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure, PDB code: 6dlr was solved by A.Peselis, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.54 / 2.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.520, 92.677, 74.487, 90.00, 121.21, 90.00
R / Rfree (%) 19.7 / 22.2

Other elements in 6dlr:

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Potassium (K) 3 atoms

Iridium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iridium atom in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure (pdb code 6dlr). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 18 binding sites of Iridium where determined in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure, PDB code: 6dlr:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 1 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir202

b:78.2
occ:0.72
IR A:IRI202 0.0 78.2 0.7
N6 A:IRI202 2.2 50.7 0.7
N2 A:IRI202 2.2 48.4 0.7
N3 A:IRI202 2.3 54.9 0.7
N1 A:IRI202 2.3 52.5 0.7
N5 A:IRI202 2.3 63.5 0.7
N4 A:IRI202 2.3 39.8 0.7
O6 A:G99 4.0 52.7 1.0
OP2 A:C96 4.2 48.5 1.0
N7 A:G97 4.3 44.0 1.0
OP2 A:G95 4.4 57.4 1.0
OP1 A:G95 4.4 57.6 1.0
O6 A:G98 4.7 49.5 1.0
O4 A:PRP201 4.7 49.4 1.0
O6 A:G97 4.8 51.4 1.0
C6 A:G99 4.8 50.0 1.0
N7 A:G98 4.8 48.8 1.0
O2A A:PRP201 4.9 50.3 1.0
N4 A:IRI212 4.9 59.5 0.6
P A:G95 4.9 49.6 1.0

Iridium binding site 2 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 2 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir203

b:89.7
occ:1.00
IR A:IRI203 0.0 89.7 1.0
N1 A:IRI203 2.2 51.3 1.0
N2 A:IRI203 2.3 68.3 1.0
N5 A:IRI203 2.3 64.8 1.0
N6 A:IRI203 2.3 64.7 1.0
N4 A:IRI203 2.3 65.7 1.0
N3 A:IRI203 2.3 40.1 1.0
O6 A:G80 4.0 44.1 1.0
OP2 A:G89 4.1 47.0 1.0
N7 A:G80 4.4 49.6 1.0
OP1 A:G89 4.4 62.8 1.0
O6 A:G81 4.4 47.0 1.0
C6 A:G80 4.8 45.3 1.0
P A:G89 4.8 48.3 1.0
C5 A:G80 4.9 47.3 1.0

Iridium binding site 3 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 3 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir204

b:94.2
occ:0.71
IR A:IRI204 0.0 94.2 0.7
N4 A:IRI204 2.2 68.2 0.7
N3 A:IRI204 2.2 72.8 0.7
N6 A:IRI204 2.2 71.9 0.7
N2 A:IRI204 2.3 83.7 0.7
N1 A:IRI204 2.3 72.0 0.7
N5 A:IRI204 2.3 67.8 0.7
OP2 A:G2 3.7 78.4 1.0
O2 A:U100 3.9 69.5 1.0
O3B A:PRP201 4.0 61.9 1.0
OP2 A:A3 4.1 71.4 1.0
O6 A:G103 4.4 80.7 1.0
O6 A:G102 4.4 64.4 1.0
O3A A:PRP201 4.6 52.8 1.0
N7 A:A3 4.7 59.8 1.0
P A:G2 4.8 90.6 1.0
C2 A:U100 4.8 67.3 1.0
PB A:PRP201 4.8 57.7 1.0
O5' A:G2 4.9 78.1 1.0

Iridium binding site 4 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 4 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir205

b:91.1
occ:0.62
IR A:IRI205 0.0 91.1 0.6
N2 A:IRI205 2.2 54.9 0.6
N3 A:IRI205 2.3 77.4 0.6
N5 A:IRI205 2.3 74.2 0.6
N4 A:IRI205 2.3 54.5 0.6
N1 A:IRI205 2.3 61.4 0.6
N6 A:IRI205 2.3 58.7 0.6
OP1 A:G94 4.0 60.1 1.0
OP1 A:U7 4.0 71.5 1.0
OP1 A:G8 4.5 85.7 1.0
OP2 A:G6 4.9 64.9 1.0

Iridium binding site 5 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 5 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir206

b:62.8
occ:0.48
IR A:IRI206 0.0 62.8 0.5
N4 A:IRI206 2.2 44.5 0.5
N2 A:IRI206 2.2 42.7 0.5
N5 A:IRI206 2.2 54.6 0.5
N3 A:IRI206 2.3 60.6 0.5
N6 A:IRI206 2.3 54.1 0.5
N1 A:IRI206 2.3 60.1 0.5
OP1 A:C21 3.7 58.0 1.0
OP1 A:C33 3.9 53.6 1.0
O3' A:C20 4.4 53.2 1.0
OP2 A:C33 4.6 60.2 1.0
P A:C21 4.7 57.8 1.0
P A:C33 4.8 58.6 1.0

Iridium binding site 6 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 6 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir207

b:0.2
occ:1.00
IR A:IRI207 0.0 0.2 1.0
N4 A:IRI207 2.2 80.5 1.0
N2 A:IRI207 2.3 84.7 1.0
N1 A:IRI207 2.3 91.3 1.0
N6 A:IRI207 2.3 1.0 1.0
N5 A:IRI207 2.3 91.4 1.0
N3 A:IRI207 2.3 69.5 1.0
OP2 A:G50 3.9 71.6 1.0
OP2 A:A74 4.1 63.3 1.0
O3' A:U49 4.4 50.9 1.0
P A:G50 4.7 61.3 1.0

Iridium binding site 7 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 7 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir208

b:0.9
occ:0.79
IR A:IRI208 0.0 0.9 0.8
N1 A:IRI208 2.2 37.8 0.8
N6 A:IRI208 2.2 76.6 0.8
N4 A:IRI208 2.3 82.5 0.8
N3 A:IRI208 2.3 39.1 0.8
N2 A:IRI208 2.3 75.2 0.8
N5 A:IRI208 2.3 77.0 0.8
O6 A:G48 4.2 55.7 1.0
O6 A:G77 4.2 57.8 1.0
O6 A:G95 4.3 56.7 1.0
O1P A:PRP201 4.6 47.1 1.0

Iridium binding site 8 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 8 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir209

b:0.5
occ:0.87
IR A:IRI209 0.0 0.5 0.9
N5 A:IRI209 2.3 59.2 0.9
N2 A:IRI209 2.3 87.0 0.9
N1 A:IRI209 2.3 0.7 0.9
N6 A:IRI209 2.3 46.7 0.9
N4 A:IRI209 2.3 83.6 0.9
N3 A:IRI209 2.3 80.8 0.9
O4 A:U70 4.3 63.5 1.0
OP2 A:A55 4.6 91.4 1.0
O4 A:U71 4.7 74.3 1.0

Iridium binding site 9 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 9 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir210

b:99.4
occ:0.31
IR A:IRI210 0.0 99.4 0.3
N4 A:IRI210 2.2 63.9 0.3
N5 A:IRI210 2.2 51.4 0.3
N1 A:IRI210 2.2 55.0 0.3
N3 A:IRI210 2.3 63.4 0.3
N2 A:IRI210 2.3 62.3 0.3
N6 A:IRI210 2.3 56.1 0.3

Iridium binding site 10 out of 18 in 6dlr

Go back to Iridium Binding Sites List in 6dlr
Iridium binding site 10 out of 18 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir211

b:0.2
occ:0.54
IR A:IRI211 0.0 0.2 0.5
N5 A:IRI211 2.2 51.8 0.5
N2 A:IRI211 2.2 74.4 0.5
N3 A:IRI211 2.2 72.8 0.5
N6 A:IRI211 2.3 76.4 0.5
N4 A:IRI211 2.3 54.1 0.5
N1 A:IRI211 2.3 69.2 0.5
O6 A:G15 3.9 56.9 1.0
OP2 A:A14 4.0 67.1 1.0
N7 A:G15 4.2 53.3 1.0
O6 A:G16 4.3 54.2 1.0
OP2 A:G42 4.4 73.4 1.0
C6 A:G15 4.7 51.5 1.0
C5 A:G15 4.8 49.3 1.0

Reference:

A.Peselis, A.Serganov. Ykkc Riboswitches Employ An Add-on Helix to Adjust Specificity For Polyanionic Ligands. Nat. Chem. Biol. V. 14 887 2018.
ISSN: ESSN 1552-4469
PubMed: 30120360
DOI: 10.1038/S41589-018-0114-4
Page generated: Mon Aug 12 03:38:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy