Magnesium in PDB 6n5q: Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5q was solved by G.M.Shoffner, Z.Peng, F.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.13 / 2.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.850, 114.850, 114.650, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 18.8

The structure of Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6n5q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:89.0 occ:1.00 OP2 A:G33 2.0 89.0 1.0 OP2 A:C101 2.1 94.2 1.0 OP1 A:G100 2.3 99.2 1.0 O4 A:U102 2.4 84.3 1.0 O3' A:A99 3.2 0.1 1.0 P A:G100 3.4 98.2 1.0 P A:C101 3.4 88.8 1.0 C4 A:U102 3.5 93.7 1.0 P A:G33 3.5 80.5 1.0 OP1 A:G32 3.7 81.2 1.0 O5' A:G32 3.9 83.7 1.0 OP1 A:C101 4.0 91.2 1.0 C5 A:U102 4.1 97.5 1.0 C5' A:G100 4.2 92.6 1.0 O2' A:A99 4.2 99.4 1.0 O5' A:G100 4.2 97.4 1.0 P A:G32 4.2 81.9 1.0 O3' A:G100 4.3 88.6 1.0 O5' A:G33 4.3 80.0 1.0 O3' A:G32 4.4 75.6 1.0 OP1 A:G33 4.4 80.4 1.0 C3' A:G100 4.4 89.4 1.0 N7 A:G33 4.4 84.3 1.0 C5' A:G32 4.5 81.7 1.0 C3' A:G32 4.5 77.2 1.0 OP2 A:G32 4.5 84.3 1.0 O5' A:C101 4.5 81.5 1.0 C3' A:A99 4.6 99.1 1.0 OP2 A:G100 4.6 99.8 1.0 N3 A:U102 4.6 94.2 1.0 C8 A:G33 4.7 84.4 1.0 C2' A:A99 4.8 97.1 1.0 C4' A:G100 4.9 90.2 1.0 C5 A:C101 4.9 93.3 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:0.5 occ:1.00 OP1 A:A31 2.9 81.7 1.0 OP1 A:U49 2.9 83.2 1.0 P A:A31 4.3 76.0 1.0 P A:U49 4.3 80.7 1.0 O3' A:G48 4.9 82.8 1.0 OP2 A:A31 4.9 71.3 1.0 OP2 A:U49 5.0 76.8 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:86.5 occ:1.00 OP2 A:G100 2.5 99.8 1.0 P A:G100 3.7 98.2 1.0 OP1 A:G100 4.0 99.2 1.0 OP1 A:A34 4.1 85.7 1.0 OP2 A:A34 4.2 87.7 1.0 OP1 A:G33 4.2 80.4 1.0 N4 A:C101 4.5 98.9 1.0 N7 A:G100 4.6 99.6 1.0 P A:A34 4.6 85.9 1.0 O3' A:A99 4.6 0.1 1.0 C4' A:A99 4.8 96.4 1.0 O5' A:G100 4.9 97.4 1.0 C8 A:G100 5.0 96.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Pir-Mirna-378A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:0.5 occ:1.00 OP1 A:C7 2.8 69.3 1.0 OP1 A:A76 3.0 67.2 1.0 P A:C7 4.2 72.6 1.0 P A:A76 4.2 75.2 1.0 OP2 A:G8 4.5 64.6 1.0 O3' A:G75 4.7 74.6 1.0 OP2 A:C7 4.8 70.8 1.0 OP2 A:A76 4.8 64.1 1.0 O5' A:C7 4.9 76.1 1.0

G.M.Shoffner, Z.Peng, F.Guo. Three-Dimensional Structures of Pri-Mirna Apical Junctions and Loops Revealed By Scaffold-Directed Crystallography To Be Published.