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

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

The structure of Ddgtp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus, PDB code: 1qss 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 (°)	108.557, 108.557, 90.527, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 28.5

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

Magnesium binding site 1 out of 2 in the Ddgtp-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 Ddgtp-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 OD2 A:ASP610 2.1 18.6 1.0 O2B A:DG3113 2.3 81.4 1.0 OD2 A:ASP785 2.3 16.9 1.0 O2G A:DG3113 2.4 83.9 1.0 O A:TYR611 2.4 19.1 1.0 O2A A:DG3113 2.5 66.4 1.0 PG A:DG3113 3.0 83.3 1.0 PB A:DG3113 3.1 80.5 1.0 CG A:ASP610 3.1 18.4 1.0 O3B A:DG3113 3.2 87.0 1.0 CG A:ASP785 3.3 15.9 1.0 O3A A:DG3113 3.4 76.1 1.0 O1G A:DG3113 3.5 83.3 1.0 OD1 A:ASP610 3.5 18.6 1.0 PA A:DG3113 3.5 66.8 1.0 C A:TYR611 3.5 18.6 1.0 OD1 A:ASP785 3.5 15.8 1.0 MG A:MG1002 3.7 26.9 1.0 N A:TYR611 4.0 18.4 1.0 C A:ASP610 4.3 18.4 1.0 CA A:TYR611 4.3 18.1 1.0 CB A:ASP610 4.4 18.9 1.0 N A:SER612 4.5 18.5 1.0 O3G A:DG3113 4.5 83.8 1.0 O1B A:DG3113 4.5 81.8 1.0 C5' A:DG3113 4.5 51.8 1.0 O5' A:DG3113 4.5 61.6 1.0 N A:GLN613 4.6 18.1 1.0 CB A:ASP785 4.6 16.4 1.0 CG2 A:ILE614 4.6 17.5 1.0 O1A A:DG3113 4.6 66.7 1.0 CA A:SER612 4.6 18.8 1.0 O A:ASP610 4.7 18.6 1.0 CA A:ASP610 4.7 18.1 1.0 N A:ILE614 4.7 17.5 1.0 C A:SER612 4.8 18.6 1.0 CB A:TYR611 4.8 17.6 1.0 O A:ASP785 4.8 16.6 1.0 CB A:ILE614 5.0 17.8 1.0

Magnesium binding site 2 out of 2 in the Ddgtp-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 Ddgtp-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:26.9 occ:1.00 O2A A:DG3113 2.3 66.4 1.0 OD1 A:ASP785 2.3 15.8 1.0 O A:HOH3023 2.4 8.7 1.0 OD1 A:ASP610 2.6 18.6 1.0 O A:HOH3015 2.8 18.9 1.0 CG A:ASP610 3.1 18.4 1.0 OD2 A:ASP610 3.1 18.6 1.0 CG A:ASP785 3.4 15.9 1.0 PA A:DG3113 3.4 66.8 1.0 OE2 A:GLU786 3.6 21.5 1.0 CB A:GLU786 3.6 18.6 1.0 MG A:MG1001 3.7 2.0 1.0 C3' B:DDG112 3.8 15.3 1.0 O1A A:DG3113 3.8 66.7 1.0 OD2 A:ASP785 3.8 16.9 1.0 O A:VAL783 4.1 17.0 1.0 NZ A:LYS831 4.1 23.2 1.0 C4' B:DDG112 4.2 15.8 1.0 C A:ASP785 4.3 16.8 1.0 N A:GLU786 4.3 16.8 1.0 CB A:ASP610 4.3 18.9 1.0 O5' A:DG3113 4.3 61.6 1.0 O A:ASP785 4.5 16.6 1.0 C5' B:DDG112 4.5 16.6 1.0 CA A:GLU786 4.5 17.6 1.0 CD A:GLU786 4.5 21.5 1.0 C5' A:DG3113 4.6 51.8 1.0 N A:ASP785 4.6 16.1 1.0 CG A:GLU786 4.6 20.2 1.0 CB A:ASP785 4.6 16.4 1.0 O3A A:DG3113 4.7 76.1 1.0 CA A:ASP785 4.8 16.6 1.0 C2' B:DDG112 4.8 15.6 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