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Iridium in PDB 7eog: Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak

Protein crystallography data

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak, PDB code: 7eog was solved by K.Y.Huang, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.07 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.925, 34.771, 58.552, 90, 128.11, 90
R / Rfree (%) 19.2 / 21.8

Other elements in 7eog:

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak (pdb code 7eog). 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 the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak, PDB code: 7eog:
Jump to Iridium binding site number: 1; 2; 3;

Iridium binding site 1 out of 3 in 7eog

Go back to Iridium Binding Sites List in 7eog
Iridium binding site 1 out of 3 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


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 Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir108

b:36.5
occ:1.00
IR A:IRI108 0.0 36.5 1.0
N2 A:IRI108 2.2 23.2 1.0
N6 A:IRI108 2.3 13.0 1.0
N5 A:IRI108 2.3 15.9 1.0
N1 A:IRI108 2.3 12.4 1.0
N4 A:IRI108 2.3 11.9 1.0
N3 A:IRI108 2.3 21.6 1.0
O A:HOH265 4.0 23.1 1.0
O2' A:G9 4.0 17.0 1.0
O A:HOH297 4.3 16.8 1.0
C2' A:G9 4.6 18.6 1.0
OP1 A:G10 4.7 24.1 1.0

Iridium binding site 2 out of 3 in 7eog

Go back to Iridium Binding Sites List in 7eog
Iridium binding site 2 out of 3 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


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 Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir109

b:185.2
occ:1.00
IR A:IRI109 0.0 185.2 1.0
N6 A:IRI109 2.3 93.7 1.0
N5 A:IRI109 2.3 123.9 1.0
N2 A:IRI109 2.3 106.5 1.0
N3 A:IRI109 2.3 87.1 1.0
N4 A:IRI109 2.3 90.0 1.0
N1 A:IRI109 2.3 112.2 1.0
OP2 A:G25 4.0 87.5 1.0
N7 A:G25 4.5 66.2 1.0

Iridium binding site 3 out of 3 in 7eog

Go back to Iridium Binding Sites List in 7eog
Iridium binding site 3 out of 3 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


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 Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir110

b:168.7
occ:1.00
IR A:IRI110 0.0 168.7 1.0
N6 A:IRI110 2.3 52.4 1.0
N5 A:IRI110 2.3 77.2 1.0
N2 A:IRI110 2.3 67.6 1.0
N3 A:IRI110 2.3 73.8 1.0
N4 A:IRI110 2.3 52.2 1.0
N1 A:IRI110 2.3 37.9 1.0
O A:HOH202 3.4 39.0 1.0
O A:HOH206 4.2 43.6 1.0
C5' A:GTP101 4.3 20.4 1.0
O1A A:GTP101 4.3 29.1 1.0

Reference:

K.Huang, X.Chen, C.Li, Q.Song, H.Li, L.Zhu, Y.Yang, A.Ren. Structure-Based Investigation of Fluorogenic Pepper Aptamer. Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
PubMed: 34725509
DOI: 10.1038/S41589-021-00884-6
Page generated: Thu Nov 25 09:36:57 2021

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