Magnesium in PDB 7y7s: Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp

All present enzymatic activity of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp:
2.7.7.48;

The structure of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp, PDB code: 7y7s was solved by R.X.Cui, J.H.Gan, J.B.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.954, 120.412, 114.993, 90, 109.71, 90
R / Rfree (%)	20.8 / 24.5

The structure of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Magnesium atom in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp (pdb code 7y7s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp, PDB code: 7y7s:

Magnesium binding site 1 out of 1 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1505 b:60.7 occ:1.00 O B:HOH1652 2.2 40.9 1.0 O B:HOH1625 2.3 41.9 1.0 O B:HOH1646 2.3 57.3 1.0 O B:HOH1664 2.3 72.5 1.0 O B:GLY1005 2.5 46.6 1.0 O B:HOH1606 2.6 45.8 1.0 C B:GLY1005 3.6 50.0 1.0 O2B B:ZAN1504 4.0 63.0 1.0 CA B:GLY1005 4.1 43.6 1.0 O B:HOH1639 4.3 43.4 1.0 OD2 B:ASP1007 4.3 53.2 1.0 O1B B:ZAN1504 4.7 71.3 1.0 N B:GLY1006 4.7 43.7 1.0 PB B:ZAN1504 4.8 59.2 1.0 O B:SER1004 5.0 41.7 1.0

R.Cui, H.Li, J.Zhao, X.Li, J.Gan, J.Ma. Structural Insights Into the Dual Activities of the Two-Barrel Rna Polymerase Qde-1. Nucleic Acids Res. V. 50 10169 2022.
ISSN: ESSN 1362-4962
PubMed: 36039765
DOI: 10.1093/NAR/GKAC727