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Iridium in PDB 7oav: Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)

Protein crystallography data

The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form), PDB code: 7oav was solved by M.Mieczkowski, V.Pena, C.Hoebartner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.14 / 2.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.192, 106.76, 63.552, 90, 116.53, 90
R / Rfree (%) 20.2 / 25.5

Other elements in 7oav:

The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Potassium (K) 7 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) (pdb code 7oav). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 4 binding sites of Iridium where determined in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form), PDB code: 7oav:
Jump to Iridium binding site number: 1; 2; 3; 4;

Iridium binding site 1 out of 4 in 7oav

Go back to Iridium Binding Sites List in 7oav
Iridium binding site 1 out of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


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 Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir106

b:131.7
occ:1.00
OP2 A:G15 3.5 108.1 1.0
O4 A:U30 3.7 115.2 1.0
O6 A:G29 3.9 131.3 1.0
O6 A:G28 4.2 115.7 1.0
N7 A:G28 4.4 103.6 1.0
P A:G15 4.7 115.9 1.0
OP2 A:C16 4.8 136.8 1.0
C4 A:U30 4.8 108.0 1.0
C6 A:G28 4.9 105.2 1.0
N7 A:G29 4.9 107.5 1.0
C6 A:G29 4.9 116.9 1.0
C5 A:G28 5.0 106.3 1.0

Iridium binding site 2 out of 4 in 7oav

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Iridium binding site 2 out of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


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 Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir105

b:135.1
occ:1.00
OP2 B:G15 3.3 115.3 1.0
O6 B:G28 3.7 126.8 1.0
O4 B:U30 3.8 117.4 1.0
O6 B:G29 4.2 145.4 1.0
N7 B:G28 4.5 118.3 1.0
C6 B:G28 4.5 116.7 1.0
P B:G15 4.6 122.3 1.0
OP2 B:C16 4.7 138.3 1.0
C5 B:G28 4.8 115.6 1.0
C4 B:U30 4.9 119.5 1.0

Iridium binding site 3 out of 4 in 7oav

Go back to Iridium Binding Sites List in 7oav
Iridium binding site 3 out of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


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 Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ir104

b:122.0
occ:1.00
OP2 C:G15 3.5 101.2 1.0
O6 C:G28 3.6 107.5 1.0
O6 C:G29 3.8 140.1 1.0
O4 C:U30 3.8 102.1 1.0
N7 C:G28 4.4 109.8 1.0
OP2 C:C16 4.4 119.3 1.0
C6 C:G28 4.5 106.9 1.0
P C:G15 4.8 112.9 1.0
C5 C:G28 4.8 109.9 1.0
C6 C:G29 4.9 127.5 1.0
C4 C:U30 4.9 105.8 1.0

Iridium binding site 4 out of 4 in 7oav

Go back to Iridium Binding Sites List in 7oav
Iridium binding site 4 out of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


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 Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ir105

b:127.3
occ:1.00
OP2 D:G15 3.4 119.1 1.0
O6 D:G29 3.7 146.7 1.0
O6 D:G28 3.8 119.5 1.0
O4 D:U30 3.9 119.1 1.0
N7 D:G28 4.3 116.7 1.0
C6 D:G28 4.5 118.8 1.0
OP2 D:C16 4.6 134.4 1.0
P D:G15 4.7 122.1 1.0
C5 D:G28 4.7 117.0 1.0
C6 D:G29 4.8 134.0 1.0
C4 D:U30 4.9 115.8 1.0
OP1 D:G15 5.0 134.5 1.0

Reference:

M.Mieczkowski, C.Steinmetzger, I.Bessi, A.K.Lenz, A.Schmiedel, M.Holzapfel, C.Lambert, V.Pena, C.Hoebartner. Large Stokes Shift Fluorescence Activation in An Rna Aptamer By Intermolecular Proton Transfer to Guanine Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-23932-0
Page generated: Sat Jul 10 16:18:00 2021

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