Magnesium in PDB 6up0: Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin

The structure of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin, PDB code: 6up0 was solved by R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.41 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.284, 66.921, 76.628, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.5

The structure of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin (pdb code 6up0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin, PDB code: 6up0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:95.9 occ:1.00 OP1 C:A12 2.7 0.1 1.0 O4 C:U24 3.1 77.5 1.0 N7 C:A12 3.2 82.0 1.0 N3 C:G9 3.6 79.2 1.0 C8 C:A12 3.6 82.5 1.0 P C:A12 3.7 0.1 1.0 O4' C:G9 3.9 87.9 1.0 OP2 C:A12 3.9 94.2 1.0 C4 C:U24 4.0 78.7 1.0 N2 C:G9 4.0 74.5 1.0 C2 C:G9 4.0 77.2 1.0 O2' C:A8 4.0 86.0 1.0 C5 C:U24 4.1 79.8 1.0 O5' C:A12 4.3 96.9 1.0 C4 C:G9 4.4 76.1 1.0 C5 C:A12 4.5 75.8 1.0 C1' C:G9 4.6 85.7 1.0 C4' C:G9 4.8 85.6 1.0 N9 C:G9 4.8 77.2 1.0 C2' C:A8 4.9 87.2 1.0 N9 C:A12 5.0 77.7 1.0

Magnesium binding site 2 out of 6 in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:87.7 occ:1.00 OP1 C:A21 2.4 77.2 1.0 P C:A21 3.8 81.0 1.0 O2' C:G19 4.0 73.2 1.0 O3' C:U20 4.3 78.8 1.0 OP2 C:A21 4.7 72.1 1.0 O5' C:A21 4.7 79.7 1.0 C5' C:A21 5.0 67.7 1.0

Magnesium binding site 3 out of 6 in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg103 b:78.1 occ:1.00 OP2 C:U16 2.1 81.4 1.0 P C:U16 3.4 75.4 1.0 O3' C:A15 3.8 74.5 1.0 C5' C:U16 3.9 79.1 1.0 O5' C:U16 4.1 80.9 1.0 O4 C:U17 4.2 71.8 1.0 OP1 C:U16 4.6 82.5 1.0

Magnesium binding site 4 out of 6 in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:98.0 occ:1.00 OP1 D:A12 3.0 84.7 1.0 O4 D:U24 3.3 73.3 1.0 O2' D:A8 3.5 76.9 1.0 N7 D:A12 3.7 70.8 1.0 O4' D:G9 3.7 89.8 1.0 C5 D:U24 3.8 72.6 1.0 C4 D:U24 3.9 67.8 1.0 P D:A12 4.0 90.7 1.0 N3 D:G9 4.1 73.7 1.0 C8 D:A12 4.1 73.2 1.0 OP2 D:A12 4.2 87.6 1.0 C2' D:A8 4.4 85.0 1.0 C4' D:G9 4.5 81.3 1.0 C1' D:G9 4.7 87.7 1.0 O5' D:A12 4.7 78.2 1.0 C2 D:G9 4.7 72.3 1.0 C4 D:G9 4.8 73.5 1.0 N2 D:G9 4.8 63.8 1.0 N9 D:G9 5.0 80.1 1.0 C5' D:G9 5.0 82.4 1.0

Magnesium binding site 5 out of 6 in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:89.8 occ:1.00 OP1 D:A21 2.3 78.0 1.0 P D:A21 3.6 68.7 1.0 O5' D:A21 3.9 74.6 1.0 C15 D:YO3104 4.1 68.2 1.0 C5' D:A21 4.1 67.3 1.0 O2' D:G19 4.2 65.3 1.0 C14 D:YO3104 4.3 73.1 1.0 O3' D:U20 4.6 75.0 1.0 OP2 D:A21 4.6 71.0 1.0 C5 D:U22 4.7 67.2 1.0 O4 D:U22 4.9 71.0 1.0

Magnesium binding site 6 out of 6 in the Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Mango-III Fluorescent Aptamer Bound to YO3-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg103 b:91.3 occ:1.00 OP2 D:U16 2.5 69.4 1.0 O3' D:A15 3.2 73.5 1.0 P D:U16 3.4 77.5 1.0 O4 D:U17 3.8 66.8 1.0 O2' D:A15 3.8 66.3 1.0 C3' D:A15 4.4 69.1 1.0 OP1 D:U16 4.5 81.8 1.0 C2' D:A15 4.5 66.6 1.0 O5' D:U16 4.6 75.4 1.0 C1' D:A15 4.7 71.1 1.0 C5' D:U16 4.7 79.2 1.0 C4 D:U17 4.8 63.0 1.0

R.J.Trachman, A.R.Ferre-D'amare. Rna Aptamer Fret Pair To Be Published.