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Iridium in PDB 7elp: Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak

Protein crystallography data

The structure of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak, PDB code: 7elp was solved by X.C.Xu, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.73 / 2.79
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.465, 100.192, 40.267, 90, 90, 90
R / Rfree (%) 21.5 / 27.4

Other elements in 7elp:

The structure of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak (pdb code 7elp). 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 Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak, PDB code: 7elp:
Jump to Iridium binding site number: 1; 2; 3;

Iridium binding site 1 out of 3 in 7elp

Go back to Iridium Binding Sites List in 7elp
Iridium binding site 1 out of 3 in the Crystal Structure of Xanthine Riboswitch with Xanthine, 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 Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir102

b:126.9
occ:1.00
O6 A:G4 3.8 70.3 1.0
O4 A:U5 3.9 70.5 1.0
O4 A:U41 4.5 74.9 1.0
O6 A:G42 4.7 70.8 1.0
C4 A:U5 4.9 64.2 1.0
C6 A:G4 4.9 64.3 1.0

Iridium binding site 2 out of 3 in 7elp

Go back to Iridium Binding Sites List in 7elp
Iridium binding site 2 out of 3 in the Crystal Structure of Xanthine Riboswitch with Xanthine, 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 Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir103

b:114.8
occ:0.96
MG A:MG111 3.0 95.7 1.0
O A:HOH201 3.4 86.3 1.0
O A:HOH222 4.0 76.3 1.0
O A:HOH246 4.0 82.2 1.0
O A:HOH248 4.0 85.1 1.0
O6 A:G20 4.1 70.5 1.0
O6 A:G19 4.3 70.2 1.0
N7 A:G19 4.5 65.3 1.0
O6 A:G28 4.7 76.1 1.0
N4 A:C29 4.8 70.0 1.0
C6 A:G19 4.9 70.1 1.0
N4 A:C18 5.0 77.2 1.0
C5 A:G19 5.0 67.2 1.0

Iridium binding site 3 out of 3 in 7elp

Go back to Iridium Binding Sites List in 7elp
Iridium binding site 3 out of 3 in the Crystal Structure of Xanthine Riboswitch with Xanthine, 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 Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir102

b:99.0
occ:1.00
O4 B:U5 4.0 81.1 1.0
O4 B:U41 4.1 77.7 1.0
O6 B:G4 4.6 73.7 1.0

Reference:

X.Xu, M.Egger, H.Chen, K.Bartosik, R.Micura, A.Ren. Insights Into Xanthine Riboswitch Structure and Metal Ion-Mediated Ligand Recognition. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34125892
DOI: 10.1093/NAR/GKAB486
Page generated: Sat Jul 10 16:18:07 2021

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