Magnesium in PDB 6n5o: Structure of Human Pir-Mirna-202 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-202 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5o 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)	99.52 / 2.71
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.920, 114.920, 115.330, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 21.9

The structure of Structure of Human Pir-Mirna-202 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-202 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6n5o). 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-202 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human Pir-Mirna-202 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-202 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:64.8 occ:1.00 OP2 A:C99 2.0 0.8 1.0 OP2 A:G31 2.2 93.1 1.0 O4 A:U100 2.4 82.6 1.0 OP1 A:G98 2.5 85.9 1.0 P A:C99 3.3 85.7 1.0 C4 A:U100 3.4 85.8 1.0 P A:G31 3.7 75.9 1.0 O3' A:A97 3.7 86.8 1.0 P A:G98 3.7 87.0 1.0 OP1 A:C99 3.8 78.4 1.0 C5 A:U100 3.9 88.4 1.0 OP1 A:G30 3.9 82.7 1.0 O5' A:G30 4.0 74.3 1.0 O3' A:G98 4.2 82.0 1.0 N7 A:G31 4.2 77.8 1.0 P A:G30 4.3 75.6 1.0 O5' A:G31 4.3 76.8 1.0 O5' A:C99 4.3 81.5 1.0 OP2 A:G30 4.4 73.8 1.0 O3' A:G30 4.4 76.6 1.0 C3' A:G30 4.5 69.8 1.0 C3' A:G98 4.5 78.4 1.0 C8 A:G31 4.5 77.3 1.0 C5' A:G98 4.5 80.5 1.0 O2' A:A97 4.6 89.6 1.0 O5' A:G98 4.6 90.2 1.0 N3 A:U100 4.6 84.1 1.0 C5' A:G30 4.7 69.6 1.0 OP1 A:G31 4.8 80.2 1.0 C5 A:C99 4.9 85.1 1.0 OP2 A:G98 4.9 93.5 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Pir-Mirna-202 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-202 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:A29 3.0 72.7 1.0 OP1 A:U47 3.0 68.2 1.0 P A:A29 4.4 71.0 1.0 P A:U47 4.5 71.6 1.0 OP2 A:A29 5.0 70.3 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Pir-Mirna-202 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-202 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:88.8 occ:1.00 OP2 A:G98 2.4 93.5 1.0 P A:G98 3.6 87.0 1.0 OP1 A:G98 4.0 85.9 1.0 N7 A:G98 4.2 85.4 1.0 OP1 A:A32 4.3 80.4 1.0 N4 A:C99 4.4 84.1 1.0 OP2 A:A32 4.5 85.6 1.0 C8 A:G98 4.6 84.8 1.0 O3' A:A97 4.6 86.8 1.0 O5' A:G98 4.6 90.2 1.0 OP1 A:G31 4.7 80.2 1.0 C4' A:A97 4.9 80.8 1.0 P A:A32 4.9 76.9 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Pir-Mirna-202 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-202 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:92.0 occ:1.00 OP2 A:G8 2.9 60.6 1.0 OP1 A:C7 3.3 67.0 1.0 OP1 A:A74 3.3 70.3 1.0 O3' A:G73 3.5 72.4 1.0 P A:G8 3.8 62.5 1.0 P A:A74 3.9 72.0 1.0 OP1 A:G8 4.0 59.6 1.0 C5' A:G73 4.2 67.8 1.0 C5' A:C7 4.4 67.2 1.0 OP2 A:A74 4.4 69.8 1.0 C3' A:G73 4.5 71.3 1.0 P A:C7 4.5 68.9 1.0 O3' A:C7 4.5 62.5 1.0 OP1 A:G73 4.5 68.4 1.0 C4' A:G73 4.6 68.9 1.0 O5' A:C7 4.6 64.8 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.