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Iridium in PDB 4p9r: Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)

Protein crystallography data

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative), PDB code: 4p9r was solved by M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, B.Masquida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.95 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.440, 86.260, 109.780, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.6

Other elements in 4p9r:

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) (pdb code 4p9r). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 10 binding sites of Iridium where determined in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative), PDB code: 4p9r:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 10 in 4p9r

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Iridium binding site 1 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir601

b:54.0
occ:1.00
 IR A:IRI601 0.0 54.0 1.0
N2 A:IRI601 2.2 61.2 1.0
N6 A:IRI601 2.2 42.8 1.0
N1 A:IRI601 2.3 43.8 1.0
N4 A:IRI601 2.3 48.1 1.0
N5 A:IRI601 2.3 58.4 1.0
N3 A:IRI601 2.3 38.2 1.0
O4 A:U255 3.8 42.0 1.0
O4 A:U234 4.2 38.5 1.0
O6 A:G233 4.2 38.9 1.0
O A:HOH719 4.7 44.4 1.0
C4 A:U255 4.8 38.8 1.0
O A:HOH711 4.8 40.4 1.0
N4 A:C257 4.9 39.7 1.0
O6 A:G256 4.9 37.1 1.0

Iridium binding site 2 out of 10 in 4p9r

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Iridium binding site 2 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir602

b:57.9
occ:1.00
 IR A:IRI602 0.0 57.9 1.0
N2 A:IRI602 2.2 48.9 1.0
N6 A:IRI602 2.2 43.9 1.0
N1 A:IRI602 2.3 64.8 1.0
N5 A:IRI602 2.3 51.7 1.0
N4 A:IRI602 2.3 48.7 1.0
N3 A:IRI602 2.3 51.1 1.0
O6 A:G264 4.1 42.8 1.0
O2 A:U554 4.2 46.4 1.0
O6 A:G263 4.3 50.2 1.0
N7 A:G263 4.5 44.1 1.0

Iridium binding site 3 out of 10 in 4p9r

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Iridium binding site 3 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir603

b:76.7
occ:1.00
 IR A:IRI603 0.0 76.7 1.0
N2 A:IRI603 2.2 54.9 1.0
N6 A:IRI603 2.2 53.4 1.0
N1 A:IRI603 2.3 46.2 1.0
N5 A:IRI603 2.3 87.0 1.0
N4 A:IRI603 2.3 58.4 1.0
N3 A:IRI603 2.3 64.3 1.0
N7 A:G568 4.1 44.4 1.0
OP1 A:A570 4.2 47.0 1.0
OP2 A:A570 4.3 39.4 1.0
P A:A570 4.7 39.0 1.0
C8 A:G568 4.7 41.4 1.0
C5 A:G568 4.7 42.0 1.0
O6 A:G568 4.8 47.7 1.0

Iridium binding site 4 out of 10 in 4p9r

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Iridium binding site 4 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir604

b:0.8
occ:1.00
 IR A:IRI604 0.0 0.8 1.0
N2 A:IRI604 2.2 77.0 1.0
N6 A:IRI604 2.2 56.0 1.0
N1 A:IRI604 2.3 47.5 1.0
N5 A:IRI604 2.3 71.6 1.0
N4 A:IRI604 2.3 75.6 1.0
N3 A:IRI604 2.3 80.9 1.0
OP2 A:C336 3.6 39.5 1.0
OP2 A:G337 3.9 40.8 1.0
O2' A:A335 4.3 37.7 1.0
O3' A:A335 4.7 36.1 1.0
P A:C336 4.7 36.1 1.0
O6 A:G281 4.8 38.6 1.0
N4 A:C339 4.9 35.8 1.0
O6 A:G338 4.9 37.6 1.0

Iridium binding site 5 out of 10 in 4p9r

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Iridium binding site 5 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir605

b:0.9
occ:1.00
 IR A:IRI605 0.0 0.9 1.0
N2 A:IRI605 2.2 71.3 1.0
N6 A:IRI605 2.2 78.6 1.0
N1 A:IRI605 2.3 58.5 1.0
N5 A:IRI605 2.3 0.1 1.0
N4 A:IRI605 2.3 85.8 1.0
N3 A:IRI605 2.3 98.4 1.0
O6 A:G229 4.3 49.0 1.0
O6 A:G228 4.5 45.2 1.0
N7 A:G228 4.7 41.3 1.0

Iridium binding site 6 out of 10 in 4p9r

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Iridium binding site 6 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir606

b:0.5
occ:1.00
 IR A:IRI606 0.0 0.5 1.0
N2 A:IRI606 2.2 59.4 1.0
N6 A:IRI606 2.2 78.4 1.0
N1 A:IRI606 2.3 74.5 1.0
N5 A:IRI606 2.3 98.8 1.0
N4 A:IRI606 2.3 0.0 1.0
N3 A:IRI606 2.3 72.5 1.0
N7 A:G240 4.1 43.7 1.0
O6 A:G240 4.4 41.5 1.0
O6 A:G241 4.5 47.4 1.0
C5 A:G240 4.8 44.5 1.0
C6 A:G240 4.9 42.3 1.0

Iridium binding site 7 out of 10 in 4p9r

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Iridium binding site 7 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir607

b:0.0
occ:1.00
 IR A:IRI607 0.0 0.0 1.0
N2 A:IRI607 2.2 89.1 1.0
N6 A:IRI607 2.2 73.7 1.0
N1 A:IRI607 2.3 67.7 1.0
N5 A:IRI607 2.3 70.2 1.0
N4 A:IRI607 2.3 69.7 1.0
N3 A:IRI607 2.3 79.8 1.0
OP1 A:G323 3.7 40.5 1.0
OP1 A:C5 4.1 47.1 1.0
OP2 A:A326 4.4 55.5 1.0
O2' A:G325 4.4 51.3 1.0
O3' A:G325 4.8 56.5 1.0

Iridium binding site 8 out of 10 in 4p9r

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Iridium binding site 8 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir608

b:0.6
occ:1.00
 IR A:IRI608 0.0 0.6 1.0
N2 A:IRI608 2.2 75.2 1.0
N6 A:IRI608 2.2 69.9 1.0
N1 A:IRI608 2.3 67.7 1.0
N5 A:IRI608 2.3 0.9 1.0
N4 A:IRI608 2.3 81.8 1.0
N3 A:IRI608 2.3 67.8 1.0
O4 A:U342 4.1 50.3 1.0
O6 A:G544 4.2 52.1 1.0
O4 A:U545 4.4 59.9 1.0
N7 A:G543 4.9 61.6 1.0
C4 A:U342 4.9 49.6 1.0

Iridium binding site 9 out of 10 in 4p9r

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Iridium binding site 9 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir609

b:0.4
occ:1.00
 IR A:IRI609 0.0 0.4 1.0
N2 A:IRI609 2.2 71.6 1.0
N6 A:IRI609 2.2 69.9 1.0
N1 A:IRI609 2.3 68.8 1.0
N5 A:IRI609 2.3 95.9 1.0
N4 A:IRI609 2.3 89.6 1.0
N3 A:IRI609 2.3 94.1 1.0
N7 A:G572 4.3 44.4 1.0
O6 A:G572 4.5 43.2 1.0

Iridium binding site 10 out of 10 in 4p9r

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Iridium binding site 10 out of 10 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Heavy Atom Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir610

b:0.4
occ:1.00
 IR A:IRI610 0.0 0.4 1.0
N2 A:IRI610 2.2 90.3 1.0
N6 A:IRI610 2.2 93.7 1.0
N1 A:IRI610 2.3 72.6 1.0
N5 A:IRI610 2.3 64.5 1.0
N4 A:IRI610 2.3 65.1 1.0
N3 A:IRI610 2.3 57.6 1.0
O6 A:G296 3.8 50.8 1.0
OP1 A:A300 4.2 45.8 1.0
N7 A:G295 4.4 52.1 1.0
C6 A:G296 4.8 55.9 1.0
O6 A:G295 4.9 48.2 1.0

Reference:

M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, B.Masquida. Speciation of A Group I Intron Into A Lariat Capping Ribozyme. Proc.Natl.Acad.Sci.Usa V. 111 7659 2014.
ISSN: ESSN 1091-6490
PubMed: 24821772
DOI: 10.1073/PNAS.1322248111
Page generated: Mon Aug 12 03:28:19 2024

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