Magnesium in PDB 7y7r: Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp

All present enzymatic activity of Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp:
2.7.7.48;

The structure of Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp, PDB code: 7y7r 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)	49.57 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.366, 122.165, 114.921, 90, 109.29, 90
R / Rfree (%)	20.7 / 24.9

The structure of Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp (pdb code 7y7r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp, PDB code: 7y7r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp


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 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1504 b:33.6 occ:1.00 O A:HOH1706 2.6 39.5 1.0 O A:GLY1005 2.7 29.8 1.0 O A:HOH1801 2.8 35.1 1.0 OD2 A:ASP1007 3.0 41.0 1.0 O2B A:GTP1505 3.1 34.7 1.0 O A:HOH1690 3.2 33.5 1.0 O A:HOH1696 3.4 39.6 1.0 O1B A:GTP1505 3.5 50.8 1.0 CG A:ASP1007 3.7 28.8 1.0 O A:HOH1840 3.8 38.3 1.0 PB A:GTP1505 3.9 32.2 1.0 C A:GLY1005 3.9 24.1 1.0 CA A:CA1503 4.2 35.6 1.0 CA A:CA1502 4.2 38.6 1.0 C A:GLY1006 4.3 31.0 1.0 O A:GLY1006 4.3 22.9 1.0 OD1 A:ASP1007 4.4 28.6 1.0 CA A:GLY1006 4.4 29.9 1.0 CB A:ASP1007 4.4 22.9 1.0 N A:GLY1006 4.6 28.1 1.0 N A:ASP1007 4.7 24.9 1.0 O5' A:GTP1505 4.9 54.2 1.0 O3B A:GTP1505 4.9 50.0 1.0

Magnesium binding site 2 out of 2 in the Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1505 b:25.6 occ:1.00 O B:HOH1741 2.9 26.3 1.0 O B:GLY1005 2.9 29.4 1.0 OD2 B:ASP1007 3.0 33.3 1.0 O2B B:GTP1506 3.0 28.9 1.0 O B:HOH1654 3.0 42.1 1.0 O B:HOH1787 3.3 58.5 1.0 CG B:ASP1007 3.5 32.0 1.0 O B:HOH1763 3.6 45.2 1.0 O1B B:GTP1506 3.6 38.8 1.0 O B:HOH1772 3.7 41.8 1.0 O B:HOH1646 3.8 60.5 1.0 PB B:GTP1506 3.9 32.3 1.0 CA B:CA1504 4.0 33.3 1.0 CB B:ASP1007 4.1 25.7 1.0 C B:GLY1005 4.1 36.7 1.0 CA B:CA1503 4.2 31.0 1.0 OD1 B:ASP1007 4.2 36.3 1.0 C B:GLY1006 4.3 28.5 1.0 O B:GLY1006 4.3 30.4 1.0 CA B:GLY1006 4.5 33.0 1.0 N B:ASP1007 4.6 25.6 1.0 N B:GLY1006 4.8 27.3 1.0 O3B B:GTP1506 4.8 46.3 1.0 CA B:ASP1007 5.0 31.0 1.0 O5' B:GTP1506 5.0 57.7 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