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

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

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 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 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 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 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 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 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 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 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 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 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

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