Magnesium in PDB 6n5k: Structure of Human Pir-Mirna-449C Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

The structure of Structure of Human Pir-Mirna-449C Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5k 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)	74.85 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.960, 113.960, 114.830, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 18.6

The structure of Structure of Human Pir-Mirna-449C 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-449C Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6n5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Pir-Mirna-449C Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6n5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Pir-Mirna-449C 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-449C 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:90.4 occ:1.00 OP2 A:G30 2.1 93.3 1.0 OP2 A:C98 2.1 97.9 1.0 O4 A:U99 2.2 93.3 1.0 OP1 A:G97 2.4 97.8 1.0 C4 A:U99 3.3 96.4 1.0 P A:C98 3.5 99.6 1.0 O3' A:A96 3.5 0.3 1.0 P A:G97 3.5 0.7 1.0 P A:G30 3.6 89.3 1.0 OP1 A:G29 3.7 90.5 1.0 C5 A:U99 3.8 97.0 1.0 O5' A:G29 3.8 87.6 1.0 OP1 A:C98 4.1 90.6 1.0 P A:G29 4.1 87.0 1.0 N7 A:G30 4.2 92.8 1.0 O5' A:G30 4.2 87.3 1.0 O3' A:G97 4.3 95.8 1.0 OP2 A:G29 4.4 90.2 1.0 O3' A:G29 4.4 85.4 1.0 C3' A:G29 4.4 86.0 1.0 C5' A:G29 4.4 87.7 1.0 N3 A:U99 4.5 96.7 1.0 O5' A:C98 4.5 94.0 1.0 C8 A:G30 4.5 91.8 1.0 C5' A:G97 4.5 97.4 1.0 O5' A:G97 4.5 98.8 1.0 OP1 A:G30 4.5 88.6 1.0 C3' A:G97 4.6 97.9 1.0 OP2 A:G97 4.6 95.1 1.0 O2' A:A96 4.7 0.7 1.0 C5 A:C98 4.9 0.2 1.0 C3' A:A96 4.9 99.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Pir-Mirna-449C 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-449C 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:85.7 occ:1.00 O A:HOH303 2.4 85.7 1.0 O6 A:G8 3.0 89.5 1.0 N2 A:G2 3.3 97.0 1.0 N3 A:G2 3.4 96.3 1.0 C2 A:G2 3.8 95.6 1.0 N4 A:C7 3.8 85.2 1.0 C6 A:G8 3.9 85.2 1.0 N4 A:C6 4.1 90.6 1.0 N1 A:G8 4.2 85.3 1.0 N2 A:GTP1 4.4 94.0 1.0 OP1 A:U11 4.4 86.2 1.0 O2' A:G2 4.5 95.1 1.0 O5' A:U11 4.5 87.8 1.0 C4 A:G2 4.5 96.2 1.0 N1 A:GTP1 4.6 94.1 1.0 O4' A:U3 4.6 88.3 1.0 C1' A:G2 4.7 96.6 1.0 C2' A:G2 4.8 96.1 1.0 O6 A:G109 4.9 86.6 1.0 C2 A:GTP1 4.9 93.9 1.0 C1' A:U3 4.9 92.4 1.0 C4 A:C6 5.0 88.1 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.