Calcium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp, PDB code: 7y7q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca2001 b:30.4 occ:1.00 O A:HOH2205 2.3 27.9 1.0 OD1 A:ASP1007 2.4 34.9 1.0 OD1 A:ASP1009 2.5 29.4 1.0 O2A A:GTP2005 2.6 40.6 1.0 OD1 A:ASP1011 2.7 28.4 1.0 O2B A:GTP2005 2.7 33.2 1.0 OD2 A:ASP1009 2.8 34.2 1.0 OD2 A:ASP1007 2.8 33.9 1.0 CG A:ASP1007 3.0 25.4 1.0 CG A:ASP1009 3.0 36.1 1.0 O5' A:GTP2005 3.3 46.1 1.0 CG A:ASP1011 3.4 30.3 1.0 PA A:GTP2005 3.4 30.9 1.0 OD2 A:ASP1011 3.4 27.5 1.0 CA A:CA2002 3.7 31.7 1.0 PB A:GTP2005 3.8 28.0 1.0 O3A A:GTP2005 3.9 28.0 1.0 MG A:MG2003 4.0 23.0 1.0 O A:HOH2214 4.3 34.0 1.0 C3' D:G7 4.4 28.0 1.0 CB A:ASP1007 4.4 23.4 1.0 CB A:ASP1009 4.4 25.0 1.0 O1B A:GTP2005 4.6 33.6 1.0 N A:ASP1007 4.6 25.4 1.0 C5' A:GTP2005 4.6 33.5 1.0 CB A:ASP1011 4.7 25.0 1.0 O1A A:GTP2005 4.8 46.4 1.0 O2' D:G7 4.8 29.6 1.0 O3G A:GTP2005 4.9 30.1 1.0 N A:ASP1011 4.9 21.6 1.0 N A:ASP1009 5.0 23.0 1.0 O A:HOH2159 5.0 59.0 1.0 CA A:ASP1007 5.0 23.9 1.0

Calcium binding site 2 out of 4 in the Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca2002 b:31.7 occ:1.00 O3G A:GTP2005 2.1 30.1 1.0 O A:HOH2311 2.3 38.8 1.0 O2B A:GTP2005 2.4 33.2 1.0 OD2 A:ASP1007 2.4 33.9 1.0 O A:HOH2163 2.4 27.0 1.0 OD2 A:ASP1009 2.5 34.2 1.0 CG A:ASP1007 3.3 25.4 1.0 O A:HOH2197 3.3 49.4 1.0 PG A:GTP2005 3.4 26.9 1.0 CG A:ASP1009 3.5 36.1 1.0 O3B A:GTP2005 3.5 27.6 1.0 PB A:GTP2005 3.5 28.0 1.0 CA A:CA2001 3.7 30.4 1.0 OD1 A:ASP1007 3.8 34.9 1.0 MG A:MG2003 4.0 23.0 1.0 OD1 A:ASP709 4.1 34.3 1.0 O A:HOH2284 4.1 30.6 1.0 NZ A:LYS767 4.2 28.2 1.0 O2G A:GTP2005 4.2 28.7 1.0 CB A:ASP1009 4.2 25.0 1.0 OD2 A:ASP709 4.3 42.3 1.0 NZ A:LYS743 4.3 32.5 0.5 CB A:ASP1007 4.3 23.4 1.0 O3A A:GTP2005 4.4 28.0 1.0 OD1 A:ASP1009 4.4 29.4 1.0 O1G A:GTP2005 4.4 25.6 1.0 CG A:ASP709 4.5 36.7 1.0 O2A A:GTP2005 4.6 40.6 1.0 O1B A:GTP2005 4.7 33.6 1.0 O A:HOH2205 4.9 27.9 1.0

Calcium binding site 3 out of 4 in the Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1503 b:34.8 occ:1.00 OD1 B:ASP1009 2.4 33.5 1.0 O B:HOH1643 2.4 33.1 1.0 OD2 B:ASP1009 2.5 43.6 1.0 OD1 B:ASP1011 2.5 29.9 1.0 OD1 B:ASP1007 2.6 37.3 1.0 CG B:ASP1009 2.8 32.2 1.0 O2A B:GTP1509 2.9 68.9 1.0 O5' B:GTP1509 2.9 90.1 1.0 O2B B:GTP1509 3.0 48.0 1.0 CG B:ASP1011 3.3 37.7 1.0 OD2 B:ASP1007 3.3 41.0 1.0 CG B:ASP1007 3.3 30.6 1.0 PA B:GTP1509 3.4 69.3 1.0 OD2 B:ASP1011 3.5 31.0 1.0 O3A B:GTP1509 3.9 62.1 1.0 CA B:CA1504 3.9 39.3 1.0 PB B:GTP1509 3.9 55.1 1.0 C3' B:GTP1502 4.1 84.6 1.0 C5' B:GTP1509 4.2 80.9 1.0 CB B:ASP1009 4.3 27.5 1.0 O B:HOH1618 4.3 52.3 1.0 MG B:MG1505 4.4 32.0 1.0 C4' B:GTP1509 4.5 79.1 1.0 CB B:ASP1011 4.5 30.2 1.0 O1B B:GTP1509 4.7 63.2 1.0 CB B:ASP1007 4.7 26.8 1.0 N B:ASP1011 4.7 27.2 1.0 O2' B:GTP1502 4.8 69.8 1.0 N B:ASP1007 4.8 27.1 1.0 O1A B:GTP1509 4.8 86.1 1.0 N B:ASP1009 4.9 25.2 1.0 C2' B:GTP1502 4.9 80.9 1.0 CA B:ASP1009 5.0 25.9 1.0

Calcium binding site 4 out of 4 in the Qde-1 in Complex with Rna Template, Rna Primer and 3'-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 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:Ca1504 b:39.3 occ:1.00 O2B B:GTP1509 2.1 48.0 1.0 O B:HOH1742 2.3 31.8 1.0 O3G B:GTP1509 2.4 46.0 1.0 OD2 B:ASP1007 2.5 41.0 1.0 O B:HOH1711 2.5 42.7 1.0 OD2 B:ASP1009 2.6 43.6 1.0 PB B:GTP1509 3.2 55.1 1.0 O3B B:GTP1509 3.4 62.2 1.0 CG B:ASP1007 3.4 30.6 1.0 PG B:GTP1509 3.4 40.0 1.0 O B:HOH1834 3.7 51.4 1.0 CG B:ASP1009 3.7 32.2 1.0 MG B:MG1508 3.9 55.8 1.0 OD1 B:ASP1007 3.9 37.3 1.0 CA B:CA1503 3.9 34.8 1.0 O B:HOH1698 4.0 36.1 1.0 MG B:MG1505 4.1 32.0 1.0 O3A B:GTP1509 4.1 62.1 1.0 O2G B:GTP1509 4.2 43.0 1.0 O B:HOH1735 4.2 37.0 1.0 OD1 B:ASP709 4.3 33.6 1.0 O B:HOH1728 4.3 34.9 1.0 NZ B:LYS767 4.3 30.7 1.0 CB B:ASP1009 4.4 27.5 1.0 O1B B:GTP1509 4.4 63.2 1.0 OD2 B:ASP709 4.5 42.6 1.0 CB B:ASP1007 4.5 26.8 1.0 O1G B:GTP1509 4.6 40.7 1.0 OD1 B:ASP1009 4.6 33.5 1.0 CG B:ASP709 4.7 33.8 1.0 O2A B:GTP1509 4.9 68.9 1.0 O B:HOH1643 5.0 33.1 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