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Iridium in PDB 7jju: Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)

Protein crystallography data

The structure of Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv), PDB code: 7jju was solved by A.-L.Steckelberg, Q.Vicens, P.Auffinger, D.C.Costantino, J.C.Nix, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.72 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.190, 72.190, 137.140, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 25.3

Other elements in 7jju:

The structure of Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) also contains other interesting chemical elements:

Arsenic (As) 6 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) (pdb code 7jju). 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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv), PDB code: 7jju:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 10 in 7jju

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Iridium binding site 1 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir107

b:74.5
occ:0.62
 IR A:IRI107 0.0 74.5 0.6
N4 A:IRI107 2.1 57.8 0.6
N6 A:IRI107 2.1 51.7 0.6
N3 A:IRI107 2.1 53.2 0.6
N1 A:IRI107 2.1 66.9 0.6
N5 A:IRI107 2.1 53.6 0.6
N2 A:IRI107 2.1 63.7 0.6
O2 A:C18 4.0 56.7 1.0
O6 A:G30 4.3 54.6 1.0
N7 A:G30 4.7 41.9 1.0

Iridium binding site 2 out of 10 in 7jju

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Iridium binding site 2 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir108

b:0.9
occ:0.58
 IR A:IRI108 0.0 0.9 0.6
N1 A:IRI108 2.1 0.9 0.6
N5 A:IRI108 2.1 0.3 0.6
N4 A:IRI108 2.1 99.2 0.6
N6 A:IRI108 2.1 0.6 0.6
N2 A:IRI108 2.1 0.1 0.6
N3 A:IRI108 2.1 0.6 0.6
OP1 A:A43 3.9 73.4 1.0
O6 A:G45 4.0 78.8 1.0
N7 A:A44 4.4 81.2 1.0
OP1 A:A44 4.6 84.4 1.0
N6 A:A44 4.8 78.2 1.0
C6 A:G45 5.0 81.8 1.0

Iridium binding site 3 out of 10 in 7jju

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Iridium binding site 3 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir109

b:0.3
occ:1.00
 IR A:IRI109 0.0 0.3 1.0
N5 A:IRI109 2.1 93.7 1.0
N4 A:IRI109 2.1 80.0 1.0
N2 A:IRI109 2.1 79.1 1.0
N3 A:IRI109 2.1 0.4 1.0
N1 A:IRI109 2.1 92.2 1.0
N6 A:IRI109 2.1 0.8 1.0
OP1 A:U33 4.0 50.6 1.0
O2 B:C46 4.4 67.4 1.0
OP1 A:G34 4.6 62.2 1.0
OP2 A:G34 4.9 50.9 1.0

Iridium binding site 4 out of 10 in 7jju

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Iridium binding site 4 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir110

b:0.5
occ:0.77
 IR A:IRI110 0.0 0.5 0.8
N6 A:IRI110 2.1 0.1 0.8
N4 A:IRI110 2.1 0.0 0.8
N1 A:IRI110 2.1 0.5 0.8
N5 A:IRI110 2.1 0.7 0.8
N3 A:IRI110 2.1 87.7 0.8
N2 A:IRI110 2.1 92.2 0.8
O6 A:G2 3.9 63.7 1.0
O2G A:GTP1 4.1 0.9 1.0
N7 A:G2 4.3 61.5 1.0
C1 A:CAC106 4.3 0.2 1.0
O1A A:GTP1 4.4 0.8 1.0
N7 A:GTP1 4.7 74.6 1.0
O6 A:GTP1 4.7 67.4 1.0
C6 A:G2 4.8 57.4 1.0
C5 A:G2 4.9 61.1 1.0

Iridium binding site 5 out of 10 in 7jju

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Iridium binding site 5 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir111

b:0.8
occ:0.81
 IR A:IRI111 0.0 0.8 0.8
N1 A:IRI111 2.1 0.6 0.8
N3 A:IRI111 2.1 99.7 0.8
N6 A:IRI111 2.1 84.6 0.8
N5 A:IRI111 2.1 0.5 0.8
N4 A:IRI111 2.1 0.5 0.8
N2 A:IRI111 2.1 97.3 0.8
O6 A:G26 4.1 74.2 1.0
N7 A:G26 4.2 66.5 1.0
OP1 A:A28 4.7 67.7 1.0
C6 A:G26 4.7 64.0 1.0
C5 A:G26 4.8 59.2 1.0

Iridium binding site 6 out of 10 in 7jju

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Iridium binding site 6 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir509

b:0.1
occ:1.00
 IR B:IRI509 0.0 0.1 1.0
N1 B:IRI509 2.1 0.4 1.0
N6 B:IRI509 2.1 0.2 1.0
N4 B:IRI509 2.1 1.0 1.0
N5 B:IRI509 2.1 0.2 1.0
N3 B:IRI509 2.1 0.6 1.0
N2 B:IRI509 2.1 0.8 1.0
O2 B:CAC505 3.8 0.1 1.0
O6 B:G2 4.0 57.6 1.0
O1 B:CAC505 4.1 0.3 1.0
N7 B:G2 4.1 58.2 1.0
O1B B:GTP1 4.3 0.8 1.0
AS B:CAC505 4.6 0.7 1.0
C6 B:G2 4.8 51.0 1.0
C5 B:G2 4.9 53.9 1.0

Iridium binding site 7 out of 10 in 7jju

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Iridium binding site 7 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir510

b:83.8
occ:0.65
 IR B:IRI510 0.0 83.8 0.7
N6 B:IRI510 2.1 52.5 0.7
N3 B:IRI510 2.1 56.0 0.7
N2 B:IRI510 2.1 58.7 0.7
N4 B:IRI510 2.1 60.8 0.7
N5 B:IRI510 2.1 58.2 0.7
N1 B:IRI510 2.1 63.6 0.7
O2 B:C18 4.2 49.8 1.0
O6 B:G30 4.3 50.4 1.0
N7 B:G30 4.5 42.3 1.0

Iridium binding site 8 out of 10 in 7jju

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Iridium binding site 8 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir511

b:0.4
occ:0.29
 IR B:IRI511 0.0 0.4 0.3
N6 B:IRI511 2.1 0.6 0.3
N2 B:IRI511 2.1 0.8 0.3
N3 B:IRI511 2.1 1.0 0.3
N4 B:IRI511 2.1 0.8 0.3
N5 B:IRI511 2.1 0.8 0.3
N1 B:IRI511 2.1 0.7 0.3
OP1 B:C47 4.5 73.7 1.0
OP1 B:U48 4.9 80.6 1.0

Iridium binding site 9 out of 10 in 7jju

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Iridium binding site 9 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir512

b:0.4
occ:1.00
 IR B:IRI512 0.0 0.4 1.0
N4 B:IRI512 2.1 73.3 1.0
N5 B:IRI512 2.1 85.2 1.0
N3 B:IRI512 2.1 87.5 1.0
N1 B:IRI512 2.1 92.0 1.0
N2 B:IRI512 2.1 65.0 1.0
N6 B:IRI512 2.1 81.0 1.0
OP1 B:U33 3.9 50.2 1.0
O2 A:C46 4.1 68.0 1.0
OP1 B:G34 4.7 64.0 1.0
OP2 B:A7 4.7 60.9 1.0

Iridium binding site 10 out of 10 in 7jju

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Iridium binding site 10 out of 10 in the Crystal Structure of En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv)


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 En Exoribonuclease-Resistant Rna (Xrrna) From Potato Leafroll Virus (Plrv) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir513

b:0.3
occ:0.84
 IR B:IRI513 0.0 0.3 0.8
N6 B:IRI513 2.1 0.4 0.8
N1 B:IRI513 2.1 0.3 0.8
N4 B:IRI513 2.1 80.0 0.8
N2 B:IRI513 2.1 91.2 0.8
N5 B:IRI513 2.1 97.8 0.8
N3 B:IRI513 2.1 0.7 0.8
O6 B:G26 4.1 73.3 1.0
OP1 B:A28 4.4 70.2 1.0
N7 B:G26 4.5 65.3 1.0
C6 B:G26 4.9 64.7 1.0

Reference:

A.L.Steckelberg, Q.Vicens, D.A.Costantino, J.C.Nix, J.S.Kieft. The Crystal Structure of A Polerovirus Exoribonuclease-Resistant Rna Shows How Diverse Sequences Are Integrated Into A Conserved Fold. Rna V. 26 1767 2020.
ISSN: ESSN 1469-9001
PubMed: 32848042
DOI: 10.1261/RNA.076224.120
Page generated: Mon Aug 12 03:46:02 2024

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