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Magnesium in PDB 7oa3: Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)

Protein crystallography data

The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form), PDB code: 7oa3 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) 45.92 / 2.80
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.605, 54.026, 87.532, 90, 95.49, 90
R / Rfree (%) 22.5 / 24.1

Other elements in 7oa3:

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

Potassium (K) 4 atoms
Iridium (Ir) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) (pdb code 7oa3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form), PDB code: 7oa3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7oa3

Go back to Magnesium Binding Sites List in 7oa3
Magnesium binding site 1 out of 2 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:131.7
occ:1.00
OP2 A:C16 2.5 137.8 1.0
P A:C16 3.6 131.7 1.0
N7 A:G17 3.8 121.8 1.0
O5' A:C16 3.9 128.8 1.0
N4 A:C18 3.9 127.0 1.0
O6 A:G17 3.9 121.6 1.0
C5 A:C16 4.2 124.2 1.0
OP1 A:C16 4.2 127.8 1.0
C6 A:C16 4.5 128.3 1.0
O6 A:G29 4.6 148.6 1.0
C5 A:G17 4.6 129.8 1.0
C6 A:G17 4.6 127.1 1.0
O6 A:G31 4.7 117.3 1.0
OP2 A:G15 4.7 115.7 1.0
O4 A:U30 4.8 118.3 1.0
C8 A:G17 4.8 123.0 1.0
O3' A:G15 4.9 124.0 1.0
C4 A:C18 5.0 124.6 1.0

Magnesium binding site 2 out of 2 in 7oa3

Go back to Magnesium Binding Sites List in 7oa3
Magnesium binding site 2 out of 2 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg107

b:122.2
occ:1.00
OP2 B:G15 2.6 119.7 1.0
P B:G15 3.5 132.3 1.0
OP1 B:G15 3.6 135.3 1.0
OP2 B:C16 4.0 148.3 1.0
O2' B:G14 4.0 119.0 1.0
O4 B:U30 4.0 139.4 1.0
N1 B:G31 4.4 130.7 1.0
O5' B:G15 4.5 128.9 1.0
N2 B:G31 4.6 130.3 1.0
O3' B:G14 4.8 130.1 1.0
C2 B:G31 4.9 131.7 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: Thu Oct 3 02:52:00 2024

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