Magnesium in PDB 6wtl: Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6wtl 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)	75.49 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.34, 115.34, 115.28, 90, 90, 120
R / Rfree (%)	18.7 / 21.3

The structure of Structure of Human Pir-Mirna-19B-2 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-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6wtl). 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-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6wtl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Human Pir-Mirna-19B-2 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-19B-2 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:60.1 occ:1.00 OP2 A:G29 2.0 96.0 1.0 OP2 A:C97 2.1 100.7 1.0 O4 A:U98 2.2 85.0 1.0 OP1 A:G96 2.5 89.0 1.0 C4 A:U98 3.3 84.7 1.0 P A:C97 3.4 85.5 1.0 P A:G29 3.5 75.1 1.0 O3' A:A95 3.6 94.3 1.0 P A:G96 3.6 89.4 1.0 OP1 A:C97 3.8 83.6 1.0 C5 A:U98 3.9 86.8 1.0 OP1 A:G28 3.9 77.2 1.0 O5' A:G28 4.0 81.7 1.0 O5' A:G29 4.1 76.3 1.0 N7 A:G29 4.2 82.3 1.0 P A:G28 4.3 77.6 1.0 O3' A:G28 4.3 81.5 1.0 C5' A:G96 4.3 82.7 1.0 O3' A:G96 4.4 82.8 1.0 O5' A:C97 4.4 82.9 1.0 O5' A:G96 4.4 86.3 1.0 C3' A:G28 4.4 78.6 1.0 C8 A:G29 4.4 78.6 1.0 N3 A:U98 4.5 81.4 1.0 OP2 A:G28 4.5 82.2 1.0 OP1 A:G29 4.5 83.2 1.0 C3' A:G96 4.6 83.2 1.0 C5' A:G28 4.7 73.9 1.0 C5 A:C97 4.8 88.1 1.0 O2' A:A95 4.8 96.3 1.0 OP2 A:G96 4.9 92.5 1.0 C3' A:A95 5.0 92.0 1.0

Magnesium binding site 2 out of 4 in the Structure of Human Pir-Mirna-19B-2 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-19B-2 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:104.7 occ:1.00 OP2 A:U46 3.0 72.9 1.0 OP1 A:A27 3.1 74.3 1.0 OP1 A:U45 3.2 75.5 1.0 O3' A:G26 3.7 71.5 1.0 P A:A27 3.9 73.7 1.0 P A:U46 4.0 76.2 1.0 OP1 A:U46 4.1 79.8 1.0 C5' A:G26 4.3 67.1 1.0 OP2 A:A27 4.4 73.8 1.0 P A:U45 4.4 76.0 1.0 C5' A:U45 4.5 74.8 1.0 O5' A:U45 4.5 76.8 1.0 OP1 A:G26 4.6 69.5 1.0 O3' A:U45 4.7 72.4 1.0 C3' A:G26 4.7 66.9 1.0 C4' A:G26 4.8 70.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Human Pir-Mirna-19B-2 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-19B-2 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:79.4 occ:1.00 OP2 A:G96 2.5 92.5 1.0 P A:G96 3.5 89.4 1.0 OP1 A:G96 3.6 89.0 1.0 OP1 A:A30 4.0 81.1 1.0 OP2 A:A30 4.2 84.2 1.0 N4 A:C97 4.2 85.5 1.0 OP1 A:G29 4.3 83.2 1.0 N7 A:G96 4.3 93.8 1.0 P A:A30 4.6 78.8 1.0 O5' A:G96 4.6 86.3 1.0 O3' A:A95 4.6 94.3 1.0 C8 A:G96 4.7 89.2 1.0 C4' A:A95 4.9 90.5 1.0

Magnesium binding site 4 out of 4 in the Structure of Human Pir-Mirna-19B-2 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-19B-2 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:97.0 occ:1.00 OP1 A:C7 3.0 65.6 1.0 OP1 A:A72 3.3 68.5 1.0 P A:C7 4.5 67.9 1.0 P A:A72 4.5 72.0 1.0 OP1 A:U77 5.0 79.8 1.0 OP2 A:A72 5.0 68.5 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.