Magnesium in PDB 6n5s: Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5s 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)	75.14 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.560, 114.560, 115.060, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.1

The structure of Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem 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-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold (pdb code 6n5s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem 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-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:70.0 occ:1.00 OP2 A:C97 2.0 0.8 1.0 OP2 A:G29 2.1 0.6 1.0 O4 A:U98 2.3 90.0 1.0 OP1 A:G96 2.5 96.0 1.0 P A:C97 3.4 91.9 1.0 C4 A:U98 3.4 96.0 1.0 O3' A:A95 3.5 95.2 1.0 P A:G29 3.6 85.9 1.0 P A:G96 3.6 94.8 1.0 OP1 A:G28 3.9 89.2 1.0 O5' A:G28 3.9 84.7 1.0 C5 A:U98 3.9 0.1 1.0 OP1 A:C97 3.9 88.5 1.0 P A:G28 4.2 83.3 1.0 O3' A:G96 4.2 84.4 1.0 O5' A:G29 4.2 81.1 1.0 O2' A:A95 4.3 0.5 1.0 C5' A:G96 4.3 86.9 1.0 N7 A:G29 4.3 87.5 1.0 OP2 A:G28 4.4 75.7 1.0 O3' A:G28 4.4 77.9 1.0 O5' A:C97 4.4 88.7 1.0 O5' A:G96 4.4 98.8 1.0 C3' A:G28 4.5 79.9 1.0 C3' A:G96 4.5 78.2 1.0 N3 A:U98 4.6 89.4 1.0 C5' A:G28 4.6 77.1 1.0 OP1 A:G29 4.6 87.5 1.0 C8 A:G29 4.6 86.2 1.0 C5 A:C97 4.8 99.3 1.0 C3' A:A95 4.8 93.6 1.0 OP2 A:G96 4.8 0.5 1.0

Magnesium binding site 2 out of 5 in the Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem 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-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:1.0 occ:1.00 OP1 A:A27 2.9 84.3 1.0 OP1 A:U45 3.0 77.2 1.0 P A:A27 4.4 78.0 1.0 P A:U45 4.4 77.9 1.0 OP2 A:A27 5.0 68.0 1.0

Magnesium binding site 3 out of 5 in the Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem 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-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:88.9 occ:1.00 OP2 A:G96 2.3 0.5 1.0 P A:G96 3.5 94.8 1.0 OP1 A:G96 3.8 96.0 1.0 OP1 A:A30 4.2 87.6 1.0 N4 A:C97 4.3 94.7 1.0 OP2 A:A30 4.4 89.9 1.0 N7 A:G96 4.4 89.4 1.0 OP1 A:G29 4.4 87.5 1.0 O3' A:A95 4.5 95.2 1.0 O5' A:G96 4.6 98.8 1.0 C8 A:G96 4.7 83.8 1.0 C4' A:A95 4.8 93.1 1.0 P A:A30 4.8 85.1 1.0

Magnesium binding site 4 out of 5 in the Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem 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-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:98.8 occ:1.00 OP2 A:G8 3.0 67.6 1.0 OP1 A:C7 3.1 79.9 1.0 OP1 A:A72 3.1 77.1 1.0 O3' A:G71 3.5 77.0 1.0 P A:A72 3.8 79.4 1.0 P A:G8 3.9 70.2 1.0 OP1 A:G8 4.1 76.0 1.0 P A:C7 4.3 76.2 1.0 C5' A:C7 4.3 75.4 1.0 C5' A:G71 4.4 64.7 1.0 O5' A:C7 4.4 70.6 1.0 OP2 A:A72 4.5 71.5 1.0 C3' A:G71 4.6 70.2 1.0 O3' A:C7 4.6 70.9 1.0 C4' A:G71 4.7 70.0 1.0 OP1 A:G71 4.7 79.3 1.0

Magnesium binding site 5 out of 5 in the Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem 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 5 of Structure of Human Pir-Mirna-320B-2 Apical Loop and One-Base-Pair Stem Fused to the Ydao Riboswitch Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:0.6 occ:1.00 O A:HOH302 2.5 56.8 1.0 O6 A:G8 3.1 88.7 1.0 N2 A:G2 3.4 87.3 1.0 N4 A:C7 3.5 67.0 1.0 N3 A:G2 3.7 80.5 1.0 N4 A:C6 3.7 79.3 1.0 C6 A:G8 4.0 74.3 1.0 C2 A:G2 4.0 85.2 1.0 N1 A:G8 4.2 73.1 1.0 OP1 A:U11 4.5 92.2 1.0 C4 A:C6 4.6 74.3 1.0 O6 A:G109 4.7 77.2 1.0 O5' A:U11 4.7 77.6 1.0 O6 A:G108 4.7 77.7 1.0 O4' A:U3 4.7 78.7 1.0 O2' A:G2 4.7 88.4 1.0 C4 A:C7 4.8 77.8 1.0 N1 A:GTP1 4.8 85.3 1.0 N2 A:GTP1 4.8 83.0 1.0 C4 A:G2 4.9 78.3 1.0 C1' A:U3 5.0 79.7 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.