Magnesium in PDB 7y7q: Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp

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

The structure of Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp, PDB code: 7y7q 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)	29.31 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.211, 85.813, 101.581, 102.56, 104.05, 94.06
R / Rfree (%)	19.6 / 22.6

The structure of Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and 3'-Dgtp (pdb code 7y7q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp, PDB code: 7y7q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:23.0 occ:1.00 OD2 A:ASP1007 2.5 33.9 1.0 O A:GLY1005 2.9 29.3 1.0 O A:HOH2205 2.9 27.9 1.0 O2B A:GTP2005 3.0 33.2 1.0 O A:HOH2240 3.1 33.9 1.0 O A:HOH2159 3.2 59.0 1.0 O A:HOH2311 3.2 38.8 1.0 CG A:ASP1007 3.4 25.4 1.0 O A:HOH2410 3.7 50.5 1.0 O1B A:GTP2005 3.8 33.6 1.0 PB A:GTP2005 3.9 28.0 1.0 CA A:CA2002 4.0 31.7 1.0 CA A:CA2001 4.0 30.4 1.0 C A:GLY1005 4.1 32.7 1.0 CB A:ASP1007 4.1 23.4 1.0 C A:GLY1006 4.2 27.6 1.0 O A:HOH2404 4.2 32.8 1.0 OD1 A:ASP1007 4.3 34.9 1.0 O A:GLY1006 4.3 25.7 1.0 N A:ASP1007 4.5 25.4 1.0 CA A:GLY1006 4.5 30.2 1.0 N A:GLY1006 4.8 24.7 1.0 O3B A:GTP2005 4.8 27.6 1.0 OD2 A:ASP709 4.9 42.3 1.0 CA A:ASP1007 4.9 23.9 1.0

Magnesium binding site 2 out of 3 in the Qde-1 in Complex with Rna 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 Rna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1505 b:32.0 occ:1.00 OD2 B:ASP1007 2.7 41.0 1.0 O B:GLY1005 2.7 36.5 1.0 O B:HOH1623 3.0 64.0 1.0 O B:HOH1643 3.1 33.1 1.0 O B:HOH1766 3.2 41.3 1.0 O2B B:GTP1509 3.4 48.0 1.0 O B:HOH1711 3.6 42.7 1.0 CG B:ASP1007 3.6 30.6 1.0 C B:GLY1005 3.9 38.1 1.0 O B:HOH1827 4.0 54.9 1.0 CA B:CA1504 4.1 39.3 1.0 O1B B:GTP1509 4.1 63.2 1.0 C B:GLY1006 4.2 30.0 1.0 O B:HOH1823 4.2 38.7 1.0 PB B:GTP1509 4.3 55.1 1.0 MG B:MG1508 4.3 55.8 1.0 CA B:GLY1006 4.3 33.1 1.0 CB B:ASP1007 4.3 26.8 1.0 OD1 B:ASP1007 4.4 37.3 1.0 CA B:CA1503 4.4 34.8 1.0 O B:GLY1006 4.4 28.3 1.0 N B:ASP1007 4.5 27.1 1.0 N B:GLY1006 4.6 27.6 1.0

Magnesium binding site 3 out of 3 in the Qde-1 in Complex with Rna 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 3 of Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1508 b:55.8 occ:1.00 O3B B:GTP1509 2.2 62.2 1.0 O1B B:GTP1509 2.6 63.2 1.0 PB B:GTP1509 2.7 55.1 1.0 O B:HOH1649 2.8 61.5 1.0 O2B B:GTP1509 3.2 48.0 1.0 PG B:GTP1509 3.4 40.0 1.0 O2G B:GTP1509 3.4 43.0 1.0 O B:HOH1834 3.6 51.4 1.0 O B:HOH1623 3.8 64.0 1.0 O B:HOH1711 3.8 42.7 1.0 CA B:CA1504 3.9 39.3 1.0 O3G B:GTP1509 4.0 46.0 1.0 O3A B:GTP1509 4.2 62.1 1.0 MG B:MG1505 4.3 32.0 1.0 O1G B:GTP1509 4.5 40.7 1.0 OD2 B:ASP1116 4.8 73.6 1.0 CD B:LYS1119 5.0 54.3 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