Magnesium in PDB 6c8n: Rna-Activated 2-Aipg Monomer Complex, 2H Soaking

The structure of Rna-Activated 2-Aipg Monomer Complex, 2H Soaking, PDB code: 6c8n was solved by W.Zhang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.975, 46.975, 83.097, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 30.6

The binding sites of Magnesium atom in the Rna-Activated 2-Aipg Monomer Complex, 2H Soaking (pdb code 6c8n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Rna-Activated 2-Aipg Monomer Complex, 2H Soaking, PDB code: 6c8n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Rna-Activated 2-Aipg Monomer Complex, 2H Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna-Activated 2-Aipg Monomer Complex, 2H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:41.6 occ:1.00 O A:HOH207 2.0 34.4 1.0 O A:HOH201 4.0 28.9 1.0 O2' A:A5 4.2 38.7 1.0 C5' A:C6 4.6 32.1 1.0 O3' A:A5 4.9 32.4 1.0

Magnesium binding site 2 out of 4 in the Rna-Activated 2-Aipg Monomer Complex, 2H Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna-Activated 2-Aipg Monomer Complex, 2H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:38.9 occ:1.00 O B:HOH205 2.0 38.4 1.0 O A:HOH208 2.0 34.9 1.0 O A:HOH209 2.1 40.0 1.0 O A:HOH215 2.1 36.0 1.0 O B:HOH201 2.1 36.2 1.0 O A:HOH201 4.0 28.9 1.0 OP2 B:A5 4.2 32.0 1.0 OP1 B:LCG4 4.3 39.1 1.0 O A:HOH204 4.4 36.6 1.0 OP1 A:C6 4.5 31.7 1.0 OP2 A:U7 4.5 36.2 1.0

Magnesium binding site 3 out of 4 in the Rna-Activated 2-Aipg Monomer Complex, 2H Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna-Activated 2-Aipg Monomer Complex, 2H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:49.2 occ:0.33 O3' A:G15 2.4 32.6 0.6 O2D A:EQ1102 2.5 43.5 0.4 O2' A:G15 2.5 32.2 0.6 O3D A:EQ1102 2.8 43.1 0.4 C3' A:G15 3.3 32.0 0.6 C2' A:G15 3.3 29.9 0.6 C2D A:EQ1102 3.6 43.6 0.4 C3D A:EQ1102 3.6 44.1 0.4 C4' A:G15 3.8 32.6 0.6 C4D A:EQ1102 4.0 44.3 0.4 C1' A:G15 4.6 30.1 0.6 C1D A:EQ1102 4.7 45.1 0.4 C5' A:G15 4.7 35.2 0.6 O4D A:EQ1102 4.8 45.4 0.4 O4' A:G15 4.8 28.4 0.6 O3E A:EQ1102 4.8 45.3 0.4

Magnesium binding site 4 out of 4 in the Rna-Activated 2-Aipg Monomer Complex, 2H Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rna-Activated 2-Aipg Monomer Complex, 2H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:46.3 occ:0.33 O3' B:G15 2.3 40.7 0.6 O2D B:EQ1102 2.4 38.9 0.4 O3D B:EQ1102 2.5 43.4 0.4 O2' B:G15 2.6 36.2 0.6 C3' B:G15 3.2 37.1 0.6 C2D B:EQ1102 3.3 41.0 0.4 C2' B:G15 3.4 35.0 0.6 C3D B:EQ1102 3.4 42.3 0.4 C4' B:G15 3.7 37.8 0.6 C4D B:EQ1102 4.1 41.5 0.4 C1D B:EQ1102 4.6 40.9 0.4 C1' B:G15 4.6 34.3 0.6 C5' B:G15 4.7 39.2 0.6 O4' B:G15 4.8 34.9 0.6 O4D B:EQ1102 4.8 41.8 0.4

W.Zhang, T.Walton, L.Li, J.W.Szostak. Crystallographic Observation of Nonenzymatic Rna Primer Extension. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29851379
DOI: 10.7554/ELIFE.36422