Magnesium in PDB 7y7t: Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp

All present enzymatic activity of Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp:
2.7.7.48;

The structure of Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp, PDB code: 7y7t 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)	29.94 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.505, 85.79, 101.28, 102.38, 103.41, 94.13
R / Rfree (%)	22.1 / 25.7

The binding sites of Magnesium atom in the Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp (pdb code 7y7t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp, PDB code: 7y7t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Qde-1 in Complex with 12NT Dna Template, Atp 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 12NT Dna Template, Atp and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:91.7 occ:1.00 O A:HOH1676 2.3 67.0 1.0 O A:HOH1655 2.3 82.4 1.0 O2G A:GTP1501 2.3 59.9 1.0 O A:HOH1660 2.4 63.0 1.0 O A:HOH1675 2.9 61.4 1.0 PG A:GTP1501 3.5 53.2 0.7 NZ A:LYS767 3.5 41.5 1.0 O3G A:GTP1501 3.7 53.2 0.8 NH2 A:ARG671 3.8 49.8 1.0 O A:HOH1638 3.9 44.2 1.0 O3B A:GTP1501 4.1 64.0 0.7 CE A:LYS767 4.4 44.4 1.0 CD A:LYS767 4.7 40.3 1.0 O1G A:GTP1501 4.7 59.7 1.0 MG A:MG1503 4.8 63.0 1.0 CZ A:ARG671 5.0 51.2 1.0

Magnesium binding site 2 out of 5 in the Qde-1 in Complex with 12NT Dna Template, Atp 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 12NT Dna Template, Atp and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1503 b:63.0 occ:1.00 OD2 A:ASP1007 2.0 58.9 1.0 O3G A:GTP1501 2.1 53.2 0.8 O A:HOH1638 2.3 44.2 1.0 OD2 A:ASP1009 2.5 50.4 1.0 O2B A:GTP1501 2.7 64.8 1.0 O A:HOH1656 3.2 46.2 1.0 CG A:ASP1007 3.2 47.7 1.0 OD1 A:ASP709 3.3 36.4 1.0 CG A:ASP1009 3.4 49.7 1.0 PG A:GTP1501 3.5 53.2 0.7 O3B A:GTP1501 3.7 64.0 0.7 O A:HOH1676 3.8 67.0 1.0 PB A:GTP1501 3.8 71.0 1.0 OD1 A:ASP1007 3.9 45.3 1.0 CB A:ASP1009 4.0 42.1 1.0 NZ A:LYS767 4.0 41.5 1.0 OD1 A:ASP1009 4.2 52.3 1.0 CG A:ASP709 4.2 43.3 1.0 CB A:ASP1007 4.3 41.5 1.0 O2G A:GTP1501 4.3 59.9 1.0 MG A:MG1504 4.4 48.7 1.0 O1G A:GTP1501 4.4 59.7 1.0 OD2 A:ASP709 4.6 59.8 1.0 O3A A:GTP1501 4.7 70.0 1.0 CE A:LYS767 4.8 44.4 1.0 O A:SER764 4.8 48.3 1.0 MG A:MG1502 4.8 91.7 1.0 O2A A:GTP1501 4.9 72.5 1.0 CA A:GLY710 5.0 36.6 1.0

Magnesium binding site 3 out of 5 in the Qde-1 in Complex with 12NT Dna Template, Atp 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 12NT Dna Template, Atp and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1504 b:48.7 occ:1.00 OD1 A:ASP1007 2.2 45.3 1.0 OD1 A:ASP1009 2.2 52.3 1.0 O A:HOH1612 2.2 57.0 1.0 OD1 A:ASP1011 2.4 60.1 1.0 O2A A:GTP1501 2.4 72.5 1.0 O2B A:GTP1501 2.8 64.8 1.0 CG A:ASP1009 3.1 49.7 1.0 CG A:ASP1011 3.1 51.4 1.0 OD2 A:ASP1011 3.1 44.5 1.0 O5' A:GTP1501 3.2 89.9 1.0 CG A:ASP1007 3.2 47.7 1.0 OD2 A:ASP1009 3.3 50.4 1.0 PA A:GTP1501 3.3 81.3 1.0 OD2 A:ASP1007 3.5 58.9 1.0 PB A:GTP1501 3.8 71.0 1.0 O3A A:GTP1501 3.8 70.0 1.0 C3' D:G3 4.2 85.9 1.0 MG A:MG1503 4.4 63.0 1.0 N A:ASP1007 4.4 45.0 1.0 CB A:ASP1009 4.4 42.1 1.0 O1B A:GTP1501 4.5 79.8 1.0 CB A:ASP1011 4.5 48.9 1.0 CB A:ASP1007 4.5 41.5 1.0 C5' A:GTP1501 4.5 78.0 1.0 N A:ASP1009 4.6 35.6 1.0 N A:ASP1011 4.6 41.1 1.0 O1A A:GTP1501 4.7 84.5 1.0 CA A:ASP1007 4.8 43.5 1.0 C A:ASP1007 4.8 45.2 1.0 CA A:ASP1009 4.8 37.0 1.0 C A:ASP1009 4.9 36.6 1.0 C4' D:G3 4.9 83.7 1.0 O A:ASP1007 4.9 48.2 1.0

Magnesium binding site 4 out of 5 in the Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1501 b:67.5 occ:1.00 OD2 B:ASP1007 2.4 53.5 1.0 OD1 B:ASP709 2.7 50.5 1.0 O1A B:ATP1503 3.0 55.9 0.2 O B:HOH1657 3.3 62.7 1.0 OD2 B:ASP1009 3.5 46.3 1.0 CG B:ASP1007 3.5 33.1 1.0 O2B B:ATP1503 3.6 45.4 1.0 CG B:ASP709 3.6 40.9 1.0 CG B:ASP1009 3.7 45.9 1.0 O B:HOH1661 3.7 61.1 1.0 NZ B:LYS767 3.7 46.8 1.0 CB B:ASP1009 3.8 40.4 1.0 O5' B:ATP1503 3.8 65.2 0.4 O B:SER764 3.9 48.2 1.0 PA B:ATP1503 3.9 58.6 0.6 CA B:GLY710 4.0 36.8 1.0 N B:GLY710 4.0 36.5 1.0 OD2 B:ASP709 4.2 53.1 1.0 C B:ASP709 4.2 38.8 1.0 OD1 B:ASP1007 4.3 35.6 1.0 OD1 B:ASP1009 4.3 45.5 1.0 O B:ASP709 4.4 36.7 1.0 O3A B:ATP1503 4.5 66.0 0.7 CB B:ASP709 4.5 44.7 1.0 CB B:ASP1007 4.5 34.7 1.0 PB B:ATP1503 4.7 56.3 0.3 CE B:LYS767 4.8 48.5 1.0 CA B:ASP709 4.9 35.8 1.0 C B:SER764 4.9 40.1 1.0 C5' B:ATP1503 5.0 56.2 1.0

Magnesium binding site 5 out of 5 in the Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Qde-1 in Complex with 12NT Dna Template, Atp and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1502 b:40.3 occ:1.00 OD1 B:ASP1007 2.1 35.6 1.0 O3G B:ATP1503 2.1 44.9 0.9 OD1 B:ASP1009 2.1 45.5 1.0 OD1 B:ASP1011 2.3 47.2 1.0 O2B B:ATP1503 2.5 45.4 1.0 OD2 B:ASP1011 2.8 33.4 1.0 CG B:ASP1011 2.9 36.7 1.0 O B:HOH1636 2.9 49.7 1.0 CG B:ASP1009 3.1 45.9 1.0 CG B:ASP1007 3.2 33.1 1.0 PG B:ATP1503 3.4 51.8 0.3 PB B:ATP1503 3.4 56.3 0.3 OD2 B:ASP1009 3.5 46.3 1.0 O3B B:ATP1503 3.5 56.2 1.0 OD2 B:ASP1007 3.6 53.5 1.0 O1B B:ATP1503 3.9 65.2 1.0 O2G B:ATP1503 4.1 52.0 0.6 N B:ASP1007 4.3 28.7 1.0 CB B:ASP1011 4.3 37.3 1.0 CB B:ASP1009 4.4 40.4 1.0 N B:ASP1009 4.5 38.5 1.0 CB B:ASP1007 4.5 34.7 1.0 O B:ASP1007 4.5 33.3 1.0 C B:ASP1007 4.5 34.5 1.0 O1G B:ATP1503 4.5 53.7 0.7 N B:ASP1011 4.6 33.3 1.0 CA B:ASP1007 4.6 37.5 1.0 CA B:ASP1009 4.8 33.9 1.0 O3A B:ATP1503 4.8 66.0 0.7 C B:ASP1009 4.9 27.1 1.0 CA B:ASP1011 4.9 27.6 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