Magnesium in PDB 1qsy: Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus

All present enzymatic activity of Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus:
2.7.7.7;

The structure of Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus, PDB code: 1qsy was solved by Y.Li, V.Mitaxov, G.Waksman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.935, 107.935, 90.237, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 27.6

The binding sites of Magnesium atom in the Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus (pdb code 1qsy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus, PDB code: 1qsy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:2.0 occ:1.00 O1G A:DDS113 2.1 86.5 1.0 OD2 A:ASP785 2.1 12.6 1.0 OD2 A:ASP610 2.2 19.0 1.0 O A:TYR611 2.2 16.9 1.0 O2B A:DDS113 2.3 80.7 1.0 O2A A:DDS113 2.4 67.0 1.0 PG A:DDS113 3.0 85.1 1.0 PB A:DDS113 3.1 79.6 1.0 O3B A:DDS113 3.1 86.3 1.0 CG A:ASP785 3.2 12.4 1.0 CG A:ASP610 3.2 17.7 1.0 C A:TYR611 3.3 17.0 1.0 OD1 A:ASP610 3.5 18.9 1.0 OD1 A:ASP785 3.6 12.0 1.0 PA A:DDS113 3.6 66.8 1.0 O3A A:DDS113 3.6 76.5 1.0 MG A:MG1002 3.7 20.9 1.0 O2G A:DDS113 3.8 86.0 1.0 N A:TYR611 4.0 16.6 1.0 O3G A:DDS113 4.1 86.4 1.0 CA A:TYR611 4.1 16.3 1.0 C A:ASP610 4.3 16.8 1.0 CG2 A:ILE614 4.3 16.1 1.0 C5' A:DDS113 4.3 53.8 1.0 N A:SER612 4.4 17.1 1.0 O5' A:DDS113 4.4 62.6 1.0 O1B A:DDS113 4.4 80.0 1.0 CB A:ASP785 4.5 11.8 1.0 CB A:ASP610 4.5 17.6 1.0 N A:GLN613 4.5 15.8 1.0 CB A:TYR611 4.5 16.1 1.0 CA A:SER612 4.5 17.1 1.0 N A:ILE614 4.6 15.6 1.0 CB A:ILE614 4.6 16.1 1.0 O A:ASP610 4.7 17.1 1.0 C A:SER612 4.7 16.6 1.0 O A:ASP785 4.7 12.7 1.0 O1A A:DDS113 4.8 66.9 1.0 CA A:ASP610 4.8 16.8 1.0

Magnesium binding site 2 out of 2 in the Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ddatp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:20.9 occ:1.00 O A:HOH3139 2.4 22.8 1.0 OD1 A:ASP785 2.4 12.0 1.0 O2A A:DDS113 2.5 67.0 1.0 OD1 A:ASP610 2.5 18.9 1.0 O B:HOH3019 2.6 9.8 1.0 CG A:ASP610 3.2 17.7 1.0 OD2 A:ASP610 3.4 19.0 1.0 CG A:ASP785 3.4 12.4 1.0 PA A:DDS113 3.5 66.8 1.0 C3' B:2DA112 3.6 15.8 1.0 MG A:MG1001 3.7 2.0 1.0 OD2 A:ASP785 3.7 12.6 1.0 O5' A:DDS113 3.9 62.6 1.0 O1A A:DDS113 4.0 66.9 1.0 CB A:GLU786 4.1 15.5 1.0 O1G A:DDS113 4.1 86.5 1.0 C4' B:2DA112 4.2 16.6 1.0 OE2 A:GLU786 4.2 17.7 1.0 C5' A:DDS113 4.2 53.8 1.0 C5' B:2DA112 4.3 17.3 1.0 O A:VAL783 4.4 13.6 1.0 CB A:ASP610 4.5 17.6 1.0 C A:ASP785 4.6 13.0 1.0 N A:GLU786 4.7 13.9 1.0 CB A:ASP785 4.8 11.8 1.0 O3A A:DDS113 4.8 76.5 1.0 OP1 B:2DA112 4.8 19.9 1.0 O A:ASP785 4.8 12.7 1.0 O5' B:2DA112 4.8 18.4 1.0 C2' B:2DA112 4.8 16.4 1.0 CA A:GLU786 4.9 14.9 1.0 CD A:GLU786 5.0 17.3 1.0

Y.Li, V.Mitaxov, G.Waksman. Structure-Based Design of Taq Dna Polymerases with Improved Properties of Dideoxynucleotide Incorporation. Proc.Natl.Acad.Sci.Usa V. 96 9491 1999.
ISSN: ISSN 0027-8424
PubMed: 10449720
DOI: 10.1073/PNAS.96.17.9491