Magnesium in PDB 6n5p: Structure of Human Pir-Mirna-340 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-340 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5p 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)	75.37 / 2.99
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.800, 114.800, 115.570, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 18.1

The structure of Structure of Human Pir-Mirna-340 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-340 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6n5p). 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-340 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human Pir-Mirna-340 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-340 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:62.8 occ:1.00 OP2 A:G32 2.0 76.8 1.0 O4 A:U101 2.1 89.9 1.0 OP2 A:C100 2.2 98.5 1.0 OP1 A:G99 2.4 0.1 1.0 C4 A:U101 3.2 88.7 1.0 O3' A:A98 3.5 0.5 1.0 P A:G32 3.5 68.3 1.0 P A:C100 3.5 80.3 1.0 P A:G99 3.5 92.8 1.0 OP1 A:G31 3.7 78.0 1.0 C5 A:U101 3.8 0.4 1.0 O5' A:G31 3.8 73.3 1.0 N7 A:G32 4.1 85.8 1.0 OP1 A:C100 4.1 82.4 1.0 O5' A:G32 4.1 64.0 1.0 P A:G31 4.2 71.7 1.0 O3' A:G31 4.2 75.9 1.0 C3' A:G31 4.3 64.3 1.0 C8 A:G32 4.3 70.6 1.0 N3 A:U101 4.4 85.3 1.0 OP2 A:G31 4.4 0.4 1.0 O3' A:G99 4.4 76.0 1.0 O5' A:G99 4.4 70.7 1.0 C5' A:G31 4.4 68.4 1.0 C5' A:G99 4.5 79.8 1.0 O2' A:A98 4.5 0.9 1.0 O5' A:C100 4.5 80.9 1.0 OP1 A:G32 4.6 73.3 1.0 C3' A:G99 4.6 77.2 1.0 OP2 A:G99 4.7 82.7 1.0 C3' A:A98 4.8 90.7 1.0 C5 A:C100 4.9 0.4 1.0 C4' A:G31 5.0 69.5 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Pir-Mirna-340 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-340 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:0.8 occ:1.00 OP1 A:A30 2.9 74.7 1.0 OP1 A:U48 3.1 74.5 1.0 P A:A30 4.3 66.2 1.0 P A:U48 4.5 73.0 1.0 OP2 A:A30 4.9 56.9 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Pir-Mirna-340 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-340 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:79.3 occ:1.00 OP2 A:G99 2.5 82.7 1.0 P A:G99 3.7 92.8 1.0 OP1 A:A33 3.8 69.6 1.0 OP1 A:G99 4.0 0.1 1.0 N4 A:C100 4.1 92.9 1.0 OP2 A:A33 4.2 68.9 1.0 N7 A:G99 4.4 88.3 1.0 OP1 A:G32 4.5 73.3 1.0 P A:A33 4.5 79.3 1.0 O5' A:G99 4.7 70.7 1.0 C8 A:G99 4.8 71.9 1.0 O3' A:A98 4.8 0.5 1.0 OP2 A:G32 5.0 76.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Pir-Mirna-340 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-340 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:0.9 occ:1.00 OP1 A:A75 3.0 67.7 1.0 OP1 A:C7 3.0 70.2 1.0 OP2 A:G8 3.0 58.6 1.0 O3' A:G74 3.5 73.5 1.0 P A:A75 3.7 72.6 1.0 O5' A:C7 4.1 66.3 1.0 P A:C7 4.1 63.8 1.0 P A:G8 4.1 62.0 1.0 C5' A:C7 4.2 69.1 1.0 OP1 A:G8 4.5 94.6 1.0 OP2 A:A75 4.5 62.7 1.0 C3' A:G74 4.7 63.6 1.0 C5' A:G74 4.7 57.6 1.0 O3' A:C7 4.8 68.9 1.0 C4' A:G74 4.9 69.0 1.0 OP1 A:G74 4.9 62.2 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.