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Iridium in PDB 7kvt: Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions

Protein crystallography data

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt was solved by L.Truong, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 2.73
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.9, 103.9, 51.699, 90, 90, 90
R / Rfree (%) 20.9 / 25.1

Other elements in 7kvt:

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Fluorine (F) 5 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions (pdb code 7kvt). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 3 binding sites of Iridium where determined in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt:
Jump to Iridium binding site number: 1; 2; 3;

Iridium binding site 1 out of 3 in 7kvt

Go back to Iridium Binding Sites List in 7kvt
Iridium binding site 1 out of 3 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions


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 Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir102

b:160.3
occ:0.56
IR B:IRI102 0.0 160.3 0.6
N2 B:IRI102 2.3 92.3 0.6
N3 B:IRI102 2.3 99.6 0.6
N6 B:IRI102 2.3 133.7 0.6
N1 B:IRI102 2.3 134.1 0.6
N4 B:IRI102 2.3 135.9 0.6
N5 B:IRI102 2.3 100.2 0.6
O6 B:G2 3.8 71.2 1.0
O6 B:G3 4.1 78.3 1.0
N7 B:G2 4.4 82.7 1.0
C6 B:G2 4.6 75.8 1.0
C5 B:G2 4.9 76.4 1.0

Iridium binding site 2 out of 3 in 7kvt

Go back to Iridium Binding Sites List in 7kvt
Iridium binding site 2 out of 3 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions


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 Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir103

b:130.6
occ:0.43
IR B:IRI103 0.0 130.6 0.4
N1 B:IRI103 2.3 85.1 0.4
N2 B:IRI103 2.3 85.9 0.4
N6 B:IRI103 2.3 95.3 0.4
N3 B:IRI103 2.3 91.1 0.4
N4 B:IRI103 2.3 95.2 0.4
N5 B:IRI103 2.3 84.5 0.4
O2' B:A17 3.6 75.4 1.0
OP2 B:U33 3.9 64.8 1.0
OP2 B:A49 4.4 71.9 1.0
OP2 B:G18 4.7 82.2 1.0
O3' B:A17 4.7 70.7 1.0
C2' B:A17 4.9 68.6 1.0

Iridium binding site 3 out of 3 in 7kvt

Go back to Iridium Binding Sites List in 7kvt
Iridium binding site 3 out of 3 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions


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 Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir104

b:148.0
occ:0.48
IR B:IRI104 0.0 148.0 0.5
N1 B:IRI104 2.3 91.7 0.5
N5 B:IRI104 2.3 90.1 0.5
N4 B:IRI104 2.3 88.3 0.5
N3 B:IRI104 2.3 105.8 0.5
N6 B:IRI104 2.3 91.1 0.5
N2 B:IRI104 2.3 92.1 0.5
O6 B:G37 4.2 84.9 1.0
O4 B:U38 4.4 89.6 1.0
O6 B:G36 4.4 82.2 1.0
N7 B:G36 4.4 81.5 1.0
N7 B:G37 4.5 79.6 1.0

Reference:

L.Truong, H.Kooshapur, S.K.Dey, X.Li, N.Tjandra, S.R.Jaffrey, A.R.Ferre-D'amare. The Fluorescent Aptamer Squash Extensively Repurposes the Adenine Riboswitch Fold. Nat.Chem.Biol. V. 18 191 2022.
ISSN: ESSN 1552-4469
PubMed: 34937911
DOI: 10.1038/S41589-021-00931-2
Page generated: Mon Aug 12 03:46:45 2024

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