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Iridium in PDB 6d3p: Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)

Protein crystallography data

The structure of Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv), PDB code: 6d3p was solved by A.-L.Steckelberg, B.M.Akiyama, D.A.Costantino, T.L.Sit, 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) 39.46 / 2.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 83.400, 83.400, 94.210, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 25.9

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) (pdb code 6d3p). 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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv), PDB code: 6d3p:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 10 in 6d3p

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Iridium binding site 1 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir101

b:0.5
occ:0.83
 IR A:IRI101 0.0 0.5 0.8
N6 A:IRI101 2.2 0.2 0.8
N1 A:IRI101 2.3 0.3 0.8
N5 A:IRI101 2.3 0.7 0.8
N2 A:IRI101 2.3 0.8 0.8
N3 A:IRI101 2.3 0.6 0.8
N4 A:IRI101 2.3 0.9 0.8
N7 A:G23 4.2 90.1 1.0
OP1 A:A25 4.3 0.7 1.0
O6 A:G23 4.5 96.0 1.0
C5 A:G23 4.8 86.1 1.0
OP2 A:A25 4.9 0.2 1.0
C6 A:G23 5.0 86.6 1.0
C8 A:G23 5.0 88.7 1.0

Iridium binding site 2 out of 10 in 6d3p

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Iridium binding site 2 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir102

b:0.4
occ:1.00
 IR A:IRI102 0.0 0.4 1.0
N2 A:IRI102 2.2 0.1 1.0
N6 A:IRI102 2.2 0.5 1.0
N3 A:IRI102 2.2 0.0 1.0
N1 A:IRI102 2.2 0.0 1.0
N4 A:IRI102 2.3 0.8 1.0
N5 A:IRI102 2.3 82.6 1.0
O6 A:G2 4.2 80.8 1.0
OP1 A:G1 4.2 79.5 1.0
N7 A:G2 4.2 77.1 1.0
O6 A:G3 4.7 66.8 1.0
C6 A:G2 4.8 82.4 1.0
C5 A:G2 4.8 80.8 1.0

Iridium binding site 3 out of 10 in 6d3p

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Iridium binding site 3 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir103

b:0.7
occ:1.00
 IR A:IRI103 0.0 0.7 1.0
N2 A:IRI103 2.2 1.0 1.0
N6 A:IRI103 2.2 0.3 1.0
N1 A:IRI103 2.2 84.0 1.0
N3 A:IRI103 2.3 0.7 1.0
N4 A:IRI103 2.3 0.6 1.0
N5 A:IRI103 2.3 0.6 1.0
OP2 A:G5 3.9 71.0 1.0
N7 A:G33 4.1 0.2 1.0
OP2 A:G32 4.4 0.7 1.0
O6 A:G33 4.5 86.7 1.0
OP2 A:G33 4.5 87.7 1.0
C5 A:G33 4.8 97.7 1.0
OP2 A:C4 4.8 66.2 1.0
C8 A:G33 4.9 0.3 1.0
OP1 A:C4 4.9 77.9 1.0
C6 A:G33 5.0 89.7 1.0

Iridium binding site 4 out of 10 in 6d3p

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Iridium binding site 4 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir104

b:92.2
occ:0.75
 IR A:IRI104 0.0 92.2 0.8
N3 A:IRI104 2.2 0.9 0.8
N1 A:IRI104 2.2 85.5 0.8
N5 A:IRI104 2.2 80.4 0.8
N4 A:IRI104 2.3 78.2 0.8
N2 A:IRI104 2.3 78.2 0.8
N6 A:IRI104 2.3 92.5 0.8
OP1 A:G29 3.6 83.6 1.0
OP2 A:A30 4.3 95.7 1.0
OP1 A:A30 4.4 80.7 1.0
P A:A30 4.8 91.1 1.0
OP1 A:U6 4.8 78.9 1.0
P A:G29 4.9 74.4 1.0
O2' A:A28 5.0 90.9 1.0

Iridium binding site 5 out of 10 in 6d3p

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Iridium binding site 5 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir105

b:0.6
occ:1.00
 IR A:IRI105 0.0 0.6 1.0
N6 A:IRI105 2.2 0.7 1.0
N2 A:IRI105 2.2 0.3 1.0
N1 A:IRI105 2.2 0.8 1.0
N4 A:IRI105 2.3 1.0 1.0
N3 A:IRI105 2.3 0.2 1.0
N5 A:IRI105 2.3 0.9 1.0
OP1 A:G23 4.4 0.5 1.0
OP2 A:G23 4.6 99.9 1.0
P A:G23 5.0 88.0 1.0

Iridium binding site 6 out of 10 in 6d3p

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Iridium binding site 6 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir106

b:83.5
occ:1.00
 IR A:IRI106 0.0 83.5 1.0
N3 A:IRI106 2.3 89.3 1.0
N5 A:IRI106 2.3 80.8 1.0
N2 A:IRI106 2.3 77.0 1.0
N6 A:IRI106 2.3 80.5 1.0
N4 A:IRI106 2.3 83.1 1.0
N1 A:IRI106 2.3 0.7 1.0
O6 A:G20 4.0 91.0 1.0
N7 A:G20 4.5 80.9 1.0
O4 A:U21 4.7 75.4 1.0
C6 A:G20 4.8 75.9 1.0

Iridium binding site 7 out of 10 in 6d3p

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Iridium binding site 7 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir107

b:98.9
occ:0.58
 IR A:IRI107 0.0 98.9 0.6
N5 A:IRI107 2.2 87.4 0.6
N3 A:IRI107 2.2 0.7 0.6
N4 A:IRI107 2.3 88.1 0.6
N6 A:IRI107 2.3 89.6 0.6
N1 A:IRI107 2.3 98.0 0.6
N2 A:IRI107 2.3 87.0 0.6
O6 A:G32 4.2 94.8 1.0
O6 A:G33 4.2 86.7 1.0
N7 A:G31 4.3 0.6 1.0
O6 A:G31 4.6 0.6 1.0
N7 A:G32 4.8 99.7 1.0
C6 A:G33 4.9 89.7 1.0

Iridium binding site 8 out of 10 in 6d3p

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Iridium binding site 8 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir108

b:73.9
occ:0.61
 IR A:IRI108 0.0 73.9 0.6
N3 A:IRI108 2.2 78.3 0.6
N4 A:IRI108 2.3 73.7 0.6
N5 A:IRI108 2.3 57.8 0.6
N6 A:IRI108 2.3 77.3 0.6
N1 A:IRI108 2.3 58.2 0.6
N2 A:IRI108 2.3 80.2 0.6
O6 A:G18 4.4 80.1 1.0
N7 A:G18 4.5 80.4 1.0

Iridium binding site 9 out of 10 in 6d3p

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Iridium binding site 9 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir109

b:0.5
occ:0.66
 IR A:IRI109 0.0 0.5 0.7
N5 A:IRI109 2.2 0.6 0.7
N3 A:IRI109 2.3 0.3 0.7
N6 A:IRI109 2.3 1.0 0.7
N4 A:IRI109 2.3 0.6 0.7
N1 A:IRI109 2.3 0.8 0.7
N2 A:IRI109 2.3 0.4 0.7
O2 A:U15 3.7 0.2 1.0
C2 A:U15 4.8 0.7 1.0
OP1 A:C17 5.0 98.2 1.0

Iridium binding site 10 out of 10 in 6d3p

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Iridium binding site 10 out of 10 in the Crystal Structure of An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv)


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 An Exoribonuclease-Resistant Rna From Sweet Clover Necrotic Mosaic Virus (Scnmv) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir110

b:0.1
occ:0.74
 IR A:IRI110 0.0 0.1 0.7
N1 A:IRI110 2.2 0.9 0.7
N5 A:IRI110 2.2 0.8 0.7
N6 A:IRI110 2.2 0.8 0.7
N4 A:IRI110 2.3 0.7 0.7
N3 A:IRI110 2.3 0.9 0.7
N2 A:IRI110 2.3 0.7 0.7

Reference:

A.L.Steckelberg, B.M.Akiyama, D.A.Costantino, T.L.Sit, J.C.Nix, J.S.Kieft. A Folded Viral Noncoding Rna Blocks Host Cell Exoribonucleases Through A Conformationally Dynamic Rna Structure. Proc. Natl. Acad. Sci. V. 115 6404 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29866852
DOI: 10.1073/PNAS.1802429115
Page generated: Sun Dec 13 22:40:32 2020

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