Calcium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Qde-1 in Complex with Dna Template, Rna Primer and 3'-Dgtp, PDB code: 7y7r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Qde-1 in Complex with Dna 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 Dna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1502 b:38.6 occ:1.00 O2A A:GTP1505 2.3 44.8 1.0 O A:HOH1801 2.3 35.1 1.0 OD1 A:ASP1007 2.4 28.6 1.0 OD1 A:ASP1009 2.4 33.6 1.0 OD1 A:ASP1011 2.6 32.6 1.0 O2B A:GTP1505 3.0 34.7 1.0 OD2 A:ASP1009 3.0 46.0 1.0 CG A:ASP1009 3.1 30.4 1.0 CG A:ASP1007 3.2 28.8 1.0 OD2 A:ASP1007 3.3 41.0 1.0 CG A:ASP1011 3.3 31.5 1.0 O5' A:GTP1505 3.4 54.2 1.0 PA A:GTP1505 3.4 41.3 1.0 OD2 A:ASP1011 3.5 24.1 1.0 CA A:CA1503 3.5 35.6 1.0 C3' D:G7 4.1 40.9 1.0 PB A:GTP1505 4.2 32.2 1.0 MG A:MG1504 4.2 33.6 1.0 O3A A:GTP1505 4.2 37.5 1.0 CB A:ASP1009 4.5 26.9 1.0 O1A A:GTP1505 4.6 42.8 1.0 C5' A:GTP1505 4.6 35.2 1.0 CB A:ASP1007 4.6 22.9 1.0 N A:ASP1007 4.6 24.9 1.0 O2' D:G7 4.6 30.0 1.0 CB A:ASP1011 4.7 24.3 1.0 C2' D:G7 4.8 36.9 1.0 O1B A:GTP1505 4.8 50.8 1.0 N A:ASP1009 4.9 25.9 1.0 N A:ASP1011 4.9 23.9 1.0 C4' D:G7 5.0 40.6 1.0

Calcium binding site 2 out of 4 in the Qde-1 in Complex with Dna 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 Dna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1503 b:35.6 occ:1.00 O2B A:GTP1505 2.2 34.7 1.0 O3G A:GTP1505 2.2 27.5 1.0 O A:HOH1661 2.4 36.0 1.0 OD2 A:ASP1009 2.4 46.0 1.0 O A:HOH1696 2.4 39.6 1.0 OD2 A:ASP1007 2.4 41.0 1.0 PB A:GTP1505 3.3 32.2 1.0 CG A:ASP1009 3.4 30.4 1.0 CG A:ASP1007 3.4 28.8 1.0 PG A:GTP1505 3.5 35.0 1.0 CA A:CA1502 3.5 38.6 1.0 O3B A:GTP1505 3.6 50.0 1.0 OD1 A:ASP1007 3.7 28.6 1.0 O2A A:GTP1505 3.7 44.8 1.0 O A:HOH1770 3.9 36.9 1.0 OD1 A:ASP1009 4.0 33.6 1.0 MG A:MG1504 4.2 33.6 1.0 O3A A:GTP1505 4.2 37.5 1.0 NZ A:LYS743 4.2 42.1 1.0 OD1 A:ASP709 4.2 31.1 1.0 CB A:ASP1009 4.2 26.9 1.0 NZ A:LYS767 4.4 29.2 1.0 O1G A:GTP1505 4.4 25.9 1.0 O2G A:GTP1505 4.5 38.3 1.0 O1B A:GTP1505 4.5 50.8 1.0 PA A:GTP1505 4.6 41.3 1.0 O A:HOH1801 4.6 35.1 1.0 CB A:ASP1007 4.6 22.9 1.0 CG A:ASP709 4.8 31.2 1.0 OD2 A:ASP709 4.9 39.9 1.0

Calcium binding site 3 out of 4 in the Qde-1 in Complex with Dna 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 Dna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1503 b:31.0 occ:1.00 O B:HOH1741 2.4 26.3 1.0 OD1 B:ASP1007 2.4 36.3 1.0 O2A B:GTP1506 2.5 38.3 1.0 OD1 B:ASP1009 2.5 27.3 1.0 OD1 B:ASP1011 2.5 23.8 1.0 OD2 B:ASP1009 2.7 34.4 1.0 O2B B:GTP1506 2.8 28.9 1.0 CG B:ASP1009 2.9 32.5 1.0 OD2 B:ASP1007 2.9 33.3 1.0 CG B:ASP1007 3.0 32.0 1.0 O5' B:GTP1506 3.3 57.7 1.0 CG B:ASP1011 3.4 31.2 1.0 PA B:GTP1506 3.4 43.0 1.0 OD2 B:ASP1011 3.6 30.4 1.0 CA B:CA1504 3.9 33.3 1.0 PB B:GTP1506 3.9 32.3 1.0 O3A B:GTP1506 3.9 39.1 1.0 O B:HOH1650 3.9 38.7 1.0 MG B:MG1505 4.2 25.6 1.0 C3' F:G7 4.2 49.4 1.0 CB B:ASP1009 4.4 26.8 1.0 O2' F:G7 4.5 37.2 1.0 CB B:ASP1007 4.5 25.7 1.0 O1B B:GTP1506 4.5 38.8 1.0 C5' B:GTP1506 4.6 49.3 1.0 CB B:ASP1011 4.7 27.4 1.0 O1A B:GTP1506 4.7 57.9 1.0 N B:ASP1007 4.7 25.6 1.0 N B:ASP1011 4.8 23.3 1.0 C2' F:G7 4.8 45.0 1.0 N B:ASP1009 4.9 24.5 1.0 O3G B:GTP1506 5.0 37.8 1.0

Calcium binding site 4 out of 4 in the Qde-1 in Complex with Dna 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 Dna Template, Rna Primer and 3'-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1504 b:33.3 occ:1.00 O3G B:GTP1506 2.2 37.8 1.0 OD2 B:ASP1007 2.2 33.3 1.0 O B:HOH1660 2.3 32.0 1.0 O2B B:GTP1506 2.4 28.9 1.0 OD2 B:ASP1009 2.5 34.4 1.0 O B:HOH1763 2.5 45.2 1.0 CG B:ASP1007 3.4 32.0 1.0 PG B:GTP1506 3.4 37.4 1.0 PB B:GTP1506 3.5 32.3 1.0 CG B:ASP1009 3.6 32.5 1.0 O3B B:GTP1506 3.6 46.3 1.0 CA B:CA1503 3.9 31.0 1.0 MG B:MG1505 4.0 25.6 1.0 O B:HOH1729 4.1 33.6 1.0 OD1 B:ASP1007 4.1 36.3 1.0 NZ B:LYS743 4.2 27.5 0.6 NZ B:LYS767 4.2 33.0 1.0 OD1 B:ASP709 4.2 32.5 1.0 O2G B:GTP1506 4.3 29.8 1.0 CB B:ASP1009 4.3 26.8 1.0 CB B:ASP1007 4.3 25.7 1.0 O3A B:GTP1506 4.3 39.1 1.0 O1G B:GTP1506 4.5 29.6 1.0 OD1 B:ASP1009 4.5 27.3 1.0 OD2 B:ASP709 4.6 44.4 1.0 O B:HOH1646 4.6 60.5 1.0 O1B B:GTP1506 4.6 38.8 1.0 CG B:ASP709 4.7 31.5 1.0 O2A B:GTP1506 4.8 38.3 1.0 O B:HOH1741 4.9 26.3 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