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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Dec 13 22:40:34 2020

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