Atomistry » Iridium » PDB 5e1u-7onm » 7kga
Atomistry »
  Iridium »
    PDB 5e1u-7onm »
      7kga »

Iridium in PDB 7kga: Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna

Protein crystallography data

The structure of Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna, PDB code: 7kga was solved by B.M.Akiyama, M.E.Graham, Z.O'donoghue, J.D.Beckham, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.74 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.93, 49.67, 73.46, 90, 99.74, 90
R / Rfree (%) 22.8 / 25.9

Iridium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 51;

Binding sites:

The binding sites of Iridium atom in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna (pdb code 7kga). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 51 binding sites of Iridium where determined in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna, PDB code: 7kga:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 1 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir101

b:61.1
occ:1.00
IR A:IRI101 0.0 61.1 1.0
N2 A:IRI101 2.1 40.8 1.0
N3 A:IRI101 2.1 41.5 1.0
N1 A:IRI101 2.1 47.8 1.0
N4 A:IRI101 2.1 38.1 1.0
N5 A:IRI101 2.1 39.7 1.0
N6 A:IRI101 2.1 42.6 1.0
O2' A:G62 3.9 36.5 1.0
N7 A:G64 3.9 31.8 1.0
OP2 A:A63 4.4 37.4 1.0
O6 A:G65 4.5 35.3 1.0
O6 A:G64 4.7 30.1 1.0
OP2 A:G64 4.7 47.1 1.0
C8 A:G64 4.7 32.4 1.0
C5 A:G64 4.9 29.6 1.0

Iridium binding site 2 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 2 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir102

b:40.4
occ:0.66
IR A:IRI102 0.0 40.4 0.7
N4 A:IRI102 2.1 26.5 0.7
N2 A:IRI102 2.1 27.2 0.7
N3 A:IRI102 2.1 30.0 0.7
N6 A:IRI102 2.1 29.0 0.7
N5 A:IRI102 2.1 29.1 0.7
N1 A:IRI102 2.1 33.9 0.7
O A:HOH206 3.6 31.1 1.0
O6 A:G32 4.0 29.5 1.0
OP2 A:A30 4.1 38.3 1.0
OP2 A:G31 4.1 37.6 1.0
N7 A:G31 4.2 36.5 1.0
N7 A:G32 4.5 38.5 1.0
O A:HOH235 4.6 33.3 1.0
O6 A:G31 4.9 34.0 1.0
C8 A:G31 4.9 32.9 1.0
C6 A:G32 4.9 32.6 1.0
C5 A:G31 5.0 36.8 1.0

Iridium binding site 3 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 3 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir103

b:50.5
occ:0.62
IR A:IRI103 0.0 50.5 0.6
N4 A:IRI103 2.1 35.9 0.6
N5 A:IRI103 2.1 42.8 0.6
N3 A:IRI103 2.1 45.4 0.6
N2 A:IRI103 2.1 30.1 0.6
N1 A:IRI103 2.1 49.0 0.6
N6 A:IRI103 2.1 37.1 0.6
O A:HOH237 3.8 45.3 1.0
O6 A:G17 4.2 39.8 1.0
O4 A:U18 4.6 35.1 1.0
N7 A:G17 4.6 45.9 1.0
C6 A:G17 5.0 41.2 1.0

Iridium binding site 4 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 4 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir104

b:59.3
occ:0.60
IR A:IRI104 0.0 59.3 0.6
N2 A:IRI104 1.3 56.5 0.4
N4 A:IRI104 2.1 60.4 0.6
N5 A:IRI104 2.1 54.8 0.6
N1 A:IRI104 2.1 60.6 0.6
N6 A:IRI104 2.1 54.6 0.6
N2 A:IRI104 2.1 52.4 0.6
N3 A:IRI104 2.1 47.8 0.6
N1 A:IRI104 2.4 61.1 0.4
IR A:IRI104 2.4 71.4 0.4
N5 A:IRI104 2.8 60.2 0.4
OP1 A:G26 3.5 59.3 1.0
N6 A:IRI104 3.6 57.5 0.4
OP2 A:U22 3.8 30.4 1.0
OP2 A:C27 3.9 50.0 1.0
N3 A:IRI104 3.9 55.8 0.4
OP1 A:C27 4.1 59.0 1.0
O2' A:A24 4.1 51.0 1.0
O A:HOH232 4.2 37.5 1.0
N4 A:IRI104 4.4 64.0 0.4
P A:C27 4.5 51.0 1.0
P A:G26 4.7 64.6 1.0
P A:U22 4.8 36.8 1.0
OP1 A:U22 4.8 39.4 1.0
OP2 A:C23 4.9 42.0 1.0

Iridium binding site 5 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 5 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir104

b:71.4
occ:0.40
IR A:IRI104 0.0 71.4 0.4
N4 A:IRI104 1.3 60.4 0.6
N1 A:IRI104 2.1 61.1 0.4
N6 A:IRI104 2.1 57.5 0.4
N5 A:IRI104 2.1 60.2 0.4
N2 A:IRI104 2.1 56.5 0.4
N4 A:IRI104 2.1 64.0 0.4
N3 A:IRI104 2.1 55.8 0.4
N6 A:IRI104 2.2 54.6 0.6
IR A:IRI104 2.4 59.3 0.6
N1 A:IRI104 3.0 60.6 0.6
N3 A:IRI104 3.4 47.8 0.6
OP1 A:G26 3.5 59.3 1.0
N5 A:IRI104 4.0 54.8 0.6
OP1 A:U22 4.0 39.4 1.0
OP2 A:A25 4.3 61.6 1.0
N2 A:IRI104 4.4 52.4 0.6
O2' A:A24 4.4 51.0 1.0
OP2 A:U22 4.5 30.4 1.0
OP2 A:C23 4.6 42.0 1.0
O3' A:A24 4.7 62.4 1.0
P A:U22 4.8 36.8 1.0
P A:G26 4.9 64.6 1.0

Iridium binding site 6 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 6 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir105

b:64.1
occ:0.52
IR A:IRI105 0.0 64.1 0.5
N2 A:IRI105 2.1 58.6 0.5
N5 A:IRI105 2.1 50.8 0.5
N6 A:IRI105 2.1 55.2 0.5
N3 A:IRI105 2.1 66.3 0.5
N4 A:IRI105 2.1 46.3 0.5
N1 A:IRI105 2.1 52.9 0.5
O A:HOH205 3.6 46.5 1.0
O A:HOH216 4.0 52.5 1.0
N7 A:G87 4.3 37.5 1.0
O6 A:G87 4.4 29.7 1.0
N7 A:A86 4.9 40.7 1.0
N1 A:A24 5.0 50.5 1.0

Iridium binding site 7 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 7 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir106

b:44.3
occ:0.41
IR A:IRI106 0.0 44.3 0.4
N2 A:IRI106 2.1 39.8 0.4
N5 A:IRI106 2.1 40.8 0.4
N4 A:IRI106 2.1 47.7 0.4
N3 A:IRI106 2.1 41.9 0.4
N1 A:IRI106 2.1 43.1 0.4
N6 A:IRI106 2.1 37.9 0.4
OP1 A:A61 3.7 38.9 1.0
OP2 A:G62 4.0 45.1 1.0
P A:A61 4.8 40.4 1.0
OP2 A:A61 4.8 40.1 1.0
OP1 A:G62 4.9 49.0 1.0
P A:G62 5.0 42.6 1.0

Iridium binding site 8 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 8 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir107

b:63.8
occ:0.39
IR A:IRI107 0.0 63.8 0.4
N3 A:IRI107 2.1 50.2 0.4
N6 A:IRI107 2.1 58.8 0.4
N4 A:IRI107 2.1 48.6 0.4
N1 A:IRI107 2.1 43.4 0.4
N2 A:IRI107 2.1 43.8 0.4
N5 A:IRI107 2.1 42.9 0.4
N1 A:IRI107 2.6 41.2 0.6
N6 A:IRI107 3.1 54.6 0.6
IR A:IRI107 3.9 52.5 0.6
N7 A:G4 4.1 25.3 1.0
O6 A:G4 4.2 21.9 1.0
N2 A:IRI107 4.3 43.0 0.6
N4 A:IRI107 4.5 40.0 0.6
O6 A:G5 4.5 20.4 1.0
C5 A:G4 4.8 22.3 1.0
C6 A:G4 4.9 20.7 1.0

Iridium binding site 9 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 9 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir107

b:52.5
occ:0.61
IR A:IRI107 0.0 52.5 0.6
N1 A:IRI107 2.1 41.2 0.6
N2 A:IRI107 2.1 43.0 0.6
N6 A:IRI107 2.1 54.6 0.6
N4 A:IRI107 2.1 40.0 0.6
N5 A:IRI107 2.1 37.6 0.6
N3 A:IRI107 2.1 43.6 0.6
N3 A:IRI107 2.5 50.2 0.4
N5 A:IRI107 3.2 42.9 0.4
IR A:IRI107 3.9 63.8 0.4
O6 A:G3 4.1 24.9 1.0
N2 A:IRI107 4.1 43.8 0.4
N7 A:G3 4.3 26.1 1.0
O A:HOH233 4.6 23.6 1.0
N4 A:IRI107 4.7 48.6 0.4
O6 A:G4 4.8 21.9 1.0
C6 A:G3 4.9 21.7 1.0
N7 A:G2 4.9 24.4 1.0
O6 A:G2 4.9 22.3 1.0
C5 A:G3 5.0 22.4 1.0

Iridium binding site 10 out of 51 in 7kga

Go back to Iridium Binding Sites List in 7kga
Iridium binding site 10 out of 51 in the Crystal Structure of A Mosquito-Borne Flavivirus Dumbbell Rna


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 A Mosquito-Borne Flavivirus Dumbbell Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir108

b:136.1
occ:1.00
IR A:IRI108 0.0 136.1 1.0
N2 A:IRI108 2.1 114.0 1.0
N3 A:IRI108 2.1 108.9 1.0
N1 A:IRI108 2.1 117.5 1.0
N4 A:IRI108 2.1 111.4 1.0
N5 A:IRI108 2.1 109.1 1.0
N6 A:IRI108 2.1 127.3 1.0
O6 A:G12 3.9 62.0 1.0
O A:HOH201 3.9 46.3 1.0
N7 A:G12 4.3 63.9 1.0
O4 A:U13 4.4 61.8 1.0
C6 A:G12 4.6 60.9 1.0
C5 A:G12 4.8 63.5 1.0
O4 A:U11 4.9 63.4 1.0

Reference:

B.M.Akiyama, M.E.Graham, Z.O'donoghue, J.D.Beckham, J.S.Kieft. Three-Dimensional Structure of A Flavivirus Dumbbell Rna Reveals Molecular Details of An Rna Regulator of Replication Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
Page generated: Mon Aug 12 03:46:20 2024

Last articles

Cl in 3WTI
Cl in 3WTH
Cl in 3WSD
Cl in 3WQT
Cl in 3WS5
Cl in 3WS0
Cl in 3WS4
Cl in 3WRZ
Cl in 3WRY
Cl in 3WQC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy