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Iridium in PDB 3skl: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak

Protein crystallography data

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak, PDB code: 3skl was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.002, 34.955, 111.057, 90.00, 92.45, 90.00
R / Rfree (%) 21.9 / 26.4

Other elements in 3skl:

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Iridium Binding Sites:

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

Iridium binding site 1 out of 10 in 3skl

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Iridium binding site 1 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir402

b:0.1
occ:1.00
 IR A:IRI402 0.0 0.1 1.0
N5 A:IRI402 2.0 0.7 1.0
N4 A:IRI402 2.0 0.7 1.0
N2 A:IRI402 2.0 0.8 1.0
N6 A:IRI402 2.0 0.8 1.0
N1 A:IRI402 2.0 0.8 1.0
N3 A:IRI402 2.0 0.8 1.0
N7 A:G45 4.3 48.1 1.0
O6 A:G45 4.4 48.3 1.0
O6 A:G44 4.5 58.2 1.0
N7 A:G44 4.9 58.1 1.0

Iridium binding site 2 out of 10 in 3skl

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Iridium binding site 2 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir403

b:0.6
occ:1.00
 IR A:IRI403 0.0 0.6 1.0
N5 A:IRI403 2.0 0.4 1.0
N1 A:IRI403 2.0 0.4 1.0
N6 A:IRI403 2.0 0.4 1.0
N2 A:IRI403 2.0 0.3 1.0
N4 A:IRI403 2.0 0.2 1.0
N3 A:IRI403 2.0 0.4 1.0
O6 A:G74 4.0 48.4 1.0
O4 A:U62 4.1 48.9 1.0
OP1 A:G32 4.3 46.1 1.0
N7 A:G74 4.5 48.5 1.0
O6 A:G75 4.6 54.6 1.0
O4 A:U73 4.6 52.4 1.0
C6 A:G74 4.8 48.3 1.0
C5 A:G74 5.0 48.4 1.0

Iridium binding site 3 out of 10 in 3skl

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Iridium binding site 3 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir405

b:0.9
occ:1.00
 IR A:IRI405 0.0 0.9 1.0
N6 A:IRI405 2.0 0.9 1.0
N3 A:IRI405 2.0 0.9 1.0
N2 A:IRI405 2.0 0.7 1.0
N1 A:IRI405 2.0 0.9 1.0
N5 A:IRI405 2.0 1.0 1.0
N4 A:IRI405 2.0 0.8 1.0
OP1 A:C60 3.8 49.1 1.0
OP2 A:U48 3.8 54.2 1.0
O6 A:G32 4.0 50.1 1.0
N7 A:G32 4.1 50.0 1.0
OP2 A:C59 4.2 46.3 1.0
OP1 A:U48 4.5 54.6 1.0
P A:U48 4.6 53.8 1.0
OP1 A:C47 4.8 48.3 1.0
C6 A:G32 4.8 50.2 1.0
C5 A:G32 4.9 50.2 1.0

Iridium binding site 4 out of 10 in 3skl

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Iridium binding site 4 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir409

b:0.6
occ:1.00
 IR A:IRI409 0.0 0.6 1.0
N5 A:IRI409 2.0 0.2 1.0
N3 A:IRI409 2.0 0.2 1.0
N6 A:IRI409 2.0 0.2 1.0
N1 A:IRI409 2.0 0.3 1.0
N4 A:IRI409 2.0 0.2 1.0
N2 A:IRI409 2.0 0.2 1.0
OP2 A:G52 4.0 54.9 1.0
OP1 A:C56 4.1 56.7 1.0
OP1 A:C54 4.3 57.5 1.0
O3' A:C55 4.6 57.4 1.0
OP2 A:U51 4.6 58.8 1.0
P A:C56 5.0 56.8 1.0

Iridium binding site 5 out of 10 in 3skl

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Iridium binding site 5 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir411

b:0.0
occ:0.30
 IR A:IRI411 0.0 0.0 0.3
N3 A:IRI411 2.0 0.9 0.3
N5 A:IRI411 2.0 0.9 0.3
N2 A:IRI411 2.0 0.8 0.3
N1 A:IRI411 2.0 0.9 0.3
N4 A:IRI411 2.0 0.9 0.3
N6 A:IRI411 2.0 0.9 0.3
OP2 A:U35 4.1 64.8 1.0
OP1 A:G34 4.4 53.3 1.0
OP1 A:U35 4.5 65.2 1.0
OP1 A:U72 4.7 51.4 1.0
P A:U35 4.8 65.3 1.0

Iridium binding site 6 out of 10 in 3skl

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Iridium binding site 6 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir404

b:0.8
occ:1.00
 IR B:IRI404 0.0 0.8 1.0
N3 B:IRI404 2.0 0.5 1.0
N5 B:IRI404 2.0 0.4 1.0
N1 B:IRI404 2.0 0.4 1.0
N6 B:IRI404 2.0 0.3 1.0
N4 B:IRI404 2.0 0.4 1.0
N2 B:IRI404 2.0 0.4 1.0
OP2 B:G52 3.9 37.9 1.0
OP1 B:C56 4.0 40.2 1.0
OP1 B:C54 4.3 41.0 1.0
OP2 B:C56 4.3 40.3 1.0
OP2 B:U51 4.5 44.1 1.0
P B:C56 4.7 40.8 1.0

Iridium binding site 7 out of 10 in 3skl

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Iridium binding site 7 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir406

b:0.9
occ:0.60
 IR B:IRI406 0.0 0.9 0.6
N1 B:IRI406 2.0 0.5 1.0
N5 B:IRI406 2.0 0.5 0.6
N6 B:IRI406 2.0 0.5 0.6
N2 B:IRI406 2.0 0.5 0.6
N4 B:IRI406 2.0 0.4 0.6
N3 B:IRI406 2.0 0.5 0.6
OP1 B:C59 4.2 36.7 1.0
O3' B:G58 4.8 35.1 1.0

Iridium binding site 8 out of 10 in 3skl

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Iridium binding site 8 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir407

b:0.6
occ:1.00
 IR B:IRI407 0.0 0.6 1.0
N4 B:IRI407 2.0 0.2 1.0
N3 B:IRI407 2.0 0.2 1.0
N1 B:IRI407 2.0 0.2 1.0
N5 B:IRI407 2.0 0.2 1.0
N6 B:IRI407 2.0 0.2 1.0
N2 B:IRI407 2.0 0.3 1.0
O6 B:G45 4.1 39.7 1.0
N7 B:G45 4.4 40.7 1.0
O6 B:G44 4.6 46.4 1.0
N7 B:G44 4.8 46.1 1.0
C6 B:G45 4.9 40.2 1.0

Iridium binding site 9 out of 10 in 3skl

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Iridium binding site 9 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir408

b:0.2
occ:0.30
 IR B:IRI408 0.0 0.2 0.3
N2 B:IRI408 2.0 0.1 0.3
N4 B:IRI408 2.0 0.1 0.3
N6 B:IRI408 2.0 0.1 0.3
N3 B:IRI408 2.0 0.0 0.3
N5 B:IRI408 2.0 0.1 0.3
N1 B:IRI408 2.0 0.1 0.3
OP2 B:A31 3.6 34.7 1.0
OP1 B:A31 4.3 33.0 1.0
P B:A31 4.5 33.4 1.0
N7 B:G77 4.5 54.1 1.0
OP2 B:G77 4.9 54.6 1.0
OP2 B:A76 5.0 55.8 1.0

Iridium binding site 10 out of 10 in 3skl

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Iridium binding site 10 out of 10 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir410

b:0.3
occ:1.00
 IR B:IRI410 0.0 0.3 1.0
N2 B:IRI410 2.0 0.2 1.0
N4 B:IRI410 2.0 0.3 1.0
N5 B:IRI410 2.0 0.2 1.0
N1 B:IRI410 2.0 0.1 1.0
N6 B:IRI410 2.0 0.1 1.0
N3 B:IRI410 2.0 0.1 1.0
OP1 B:C60 3.2 43.8 1.0
OP2 B:U48 3.9 35.0 1.0
N7 B:G32 4.1 36.0 1.0
OP1 B:C47 4.1 31.4 1.0
O6 B:G32 4.5 36.0 1.0
P B:C60 4.5 43.9 1.0
OP2 B:C59 4.5 35.2 1.0
O5' B:C59 4.7 37.2 1.0
O5' B:C60 4.8 45.2 1.0
OP1 B:C59 4.8 36.7 1.0
P B:U48 4.9 34.5 1.0
P B:C59 4.9 35.7 1.0

Reference:

O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov. Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631
Page generated: Sun Dec 13 22:39:46 2020

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