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Iridium in PDB 6e80: Crystal Structure of the Corn Aptamer in Unliganded State

Protein crystallography data

The structure of Crystal Structure of the Corn Aptamer in Unliganded State, PDB code: 6e80 was solved by L.Sjekloca, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.51 / 2.90
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 93.012, 93.012, 66.560, 90.00, 90.00, 120.00
R / Rfree (%) 25.2 / 30.7

Other elements in 6e80:

The structure of Crystal Structure of the Corn Aptamer in Unliganded State also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Potassium (K) 1 atom

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of the Corn Aptamer in Unliganded State (pdb code 6e80). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 5 binding sites of Iridium where determined in the Crystal Structure of the Corn Aptamer in Unliganded State, PDB code: 6e80:
Jump to Iridium binding site number: 1; 2; 3; 4; 5;

Iridium binding site 1 out of 5 in 6e80

Go back to Iridium Binding Sites List in 6e80
Iridium binding site 1 out of 5 in the Crystal Structure of the Corn Aptamer in Unliganded State


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 the Corn Aptamer in Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir101

b:54.8
occ:1.00
IR A:IRI101 0.0 54.8 1.0
N2 A:IRI101 2.2 57.4 1.0
N6 A:IRI101 2.2 47.2 1.0
N1 A:IRI101 2.3 40.4 1.0
N5 A:IRI101 2.3 41.9 1.0
N4 A:IRI101 2.3 83.9 1.0
N3 A:IRI101 2.3 38.0 1.0
O4 A:U31 3.7 43.7 1.0
OP2 A:C30 4.0 29.8 1.0
OP2 A:A29 4.1 34.8 1.0
O5' A:A29 4.7 33.5 1.0
C4 A:U31 4.8 42.4 1.0
P A:A29 4.8 34.3 1.0

Iridium binding site 2 out of 5 in 6e80

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Iridium binding site 2 out of 5 in the Crystal Structure of the Corn Aptamer in Unliganded State


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 the Corn Aptamer in Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir102

b:0.3
occ:1.00
IR A:IRI102 0.0 0.3 1.0
N2 A:IRI102 2.2 63.9 1.0
N6 A:IRI102 2.2 71.2 1.0
N1 A:IRI102 2.3 72.1 1.0
N5 A:IRI102 2.3 48.1 1.0
N4 A:IRI102 2.3 68.5 1.0
N3 A:IRI102 2.3 64.0 1.0
O2 A:U19 4.2 45.0 1.0
OP2 A:G20 4.2 56.8 1.0
O2' A:U19 4.2 49.2 1.0

Iridium binding site 3 out of 5 in 6e80

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Iridium binding site 3 out of 5 in the Crystal Structure of the Corn Aptamer in Unliganded State


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 the Corn Aptamer in Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir103

b:0.4
occ:1.00
IR A:IRI103 0.0 0.4 1.0
N2 A:IRI103 2.2 63.1 1.0
N6 A:IRI103 2.2 51.4 1.0
N1 A:IRI103 2.3 74.0 1.0
N5 A:IRI103 2.3 61.5 1.0
N4 A:IRI103 2.3 39.6 1.0
N3 A:IRI103 2.3 68.4 1.0
OP2 A:C28 4.0 34.1 1.0
OP1 A:U27 4.6 38.8 1.0
OP2 A:U27 4.9 40.2 1.0

Iridium binding site 4 out of 5 in 6e80

Go back to Iridium Binding Sites List in 6e80
Iridium binding site 4 out of 5 in the Crystal Structure of the Corn Aptamer in Unliganded State


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 the Corn Aptamer in Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir111

b:0.9
occ:1.00
O A:HOH201 3.1 34.1 1.0
N7 A:G8 3.8 30.7 1.0
OP2 A:A7 4.0 49.0 1.0
O6 A:G8 4.3 31.5 1.0
C5 A:G8 4.7 35.3 1.0
C8 A:G8 4.8 33.8 1.0
C6 A:G8 4.8 32.6 1.0
OP2 A:G8 4.8 41.3 1.0

Iridium binding site 5 out of 5 in 6e80

Go back to Iridium Binding Sites List in 6e80
Iridium binding site 5 out of 5 in the Crystal Structure of the Corn Aptamer in Unliganded State


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 the Corn Aptamer in Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir112

b:0.9
occ:0.50
OP1 A:A11 4.0 31.5 1.0

Reference:

L.Sjekloca, A.R.Ferre-D'amare. Binding Between G Quadruplexes at the Homodimer Interface of the Corn Rna Aptamer Strongly Activates Thioflavin T Fluorescence. Cell Chem Biol V. 26 1159 2019.
ISSN: ESSN 2451-9456
PubMed: 31178406
DOI: 10.1016/J.CHEMBIOL.2019.04.012
Page generated: Sun Dec 13 22:40:36 2020

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