Magnesium in PDB 6n5n: Structure of Human Pir-Mirna-208A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-208A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5n 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)	75.11 / 2.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.680, 114.680, 114.810, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 18.6

The structure of Structure of Human Pir-Mirna-208A 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-208A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6n5n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Human Pir-Mirna-208A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Human Pir-Mirna-208A 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-208A 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:C98 2.0 0.8 1.0 OP2 A:G30 2.1 0.4 1.0 O4 A:U99 2.4 77.9 1.0 OP1 A:G97 2.5 96.5 1.0 O3' A:A96 3.2 0.4 1.0 P A:C98 3.3 86.4 1.0 P A:G97 3.4 92.6 1.0 C4 A:U99 3.4 92.8 1.0 P A:G30 3.6 76.8 1.0 OP1 A:G29 3.8 76.8 1.0 OP1 A:C98 3.9 84.6 1.0 O5' A:G29 3.9 77.1 1.0 C5' A:G97 4.0 83.0 1.0 C5 A:U99 4.0 0.3 1.0 O2' A:A96 4.1 0.5 1.0 O5' A:G97 4.1 95.3 1.0 O3' A:G97 4.2 75.5 1.0 P A:G29 4.3 76.0 1.0 O5' A:G30 4.3 73.5 1.0 C3' A:G97 4.4 77.0 1.0 O3' A:G29 4.4 76.0 1.0 O5' A:C98 4.4 82.5 1.0 OP1 A:G30 4.5 80.5 1.0 C3' A:G29 4.5 76.0 1.0 OP2 A:G29 4.5 84.0 1.0 N7 A:G30 4.6 76.3 1.0 C3' A:A96 4.6 0.1 1.0 C5' A:G29 4.6 76.0 1.0 N3 A:U99 4.6 92.7 1.0 OP2 A:G97 4.7 96.4 1.0 C4' A:G97 4.8 75.8 1.0 C5 A:C98 4.8 99.4 1.0 C8 A:G30 4.8 76.6 1.0 C2' A:A96 4.8 98.4 1.0

Magnesium binding site 2 out of 3 in the Structure of Human Pir-Mirna-208A 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-208A Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:77.2 occ:1.00 OP2 A:G97 2.6 96.4 1.0 P A:G97 3.6 92.6 1.0 OP1 A:G97 3.8 96.5 1.0 OP1 A:A31 4.0 80.0 1.0 OP2 A:A31 4.3 84.5 1.0 OP1 A:G30 4.3 80.5 1.0 N4 A:C98 4.3 97.7 1.0 N7 A:G97 4.5 97.3 1.0 O3' A:A96 4.7 0.4 1.0 P A:A31 4.7 80.4 1.0 O5' A:G97 4.8 95.3 1.0 C4' A:A96 4.9 95.6 1.0 C8 A:G97 4.9 87.9 1.0

Magnesium binding site 3 out of 3 in the Structure of Human Pir-Mirna-208A 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-208A 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:80.8 occ:1.00 O2P1 A:2BA201 4.0 79.8 1.0 O2' A:C7 4.2 62.2 1.0 O2 A:C7 4.3 76.0 1.0 C5'1 A:2BA201 4.5 66.2 1.0 O1P1 A:2BA201 4.5 84.0 1.0 N6 A:A48 4.5 77.1 1.0 P1 A:2BA201 4.6 76.4 1.0 N71 A:2BA201 4.7 59.1 1.0 N2 A:G109 4.8 74.8 1.0 C81 A:2BA201 4.8 72.1 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.