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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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
Go back to
Iridium Binding Sites List in 6d3p
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: Mon Aug 12 03:37:57 2024
|