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

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

The structure of Ddttp-Trapped Closed Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus, PDB code: 1qtm 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 (°)	107.988, 107.988, 90.201, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 28

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

Magnesium binding site 1 out of 2 in the Ddttp-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 Ddttp-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:ASP785 2.2 16.6 1.0 O1G A:TTP113 2.2 76.3 1.0 O A:TYR611 2.2 17.4 1.0 OD2 A:ASP610 2.2 19.9 1.0 O2B A:TTP113 2.2 71.6 1.0 O2A A:TTP113 2.4 60.5 1.0 PG A:TTP113 2.8 75.1 1.0 O3B A:TTP113 2.9 75.3 1.0 PB A:TTP113 3.0 71.5 1.0 CG A:ASP610 3.2 18.4 1.0 CG A:ASP785 3.2 16.9 1.0 O2G A:TTP113 3.4 76.2 1.0 C A:TYR611 3.4 16.9 1.0 OD1 A:ASP610 3.5 18.9 1.0 OD1 A:ASP785 3.6 16.4 1.0 O3A A:TTP113 3.6 68.0 1.0 PA A:TTP113 3.6 60.1 1.0 MG A:MG1002 3.7 27.1 1.0 N A:TYR611 4.0 16.5 1.0 O3G A:TTP113 4.2 76.4 1.0 CA A:TYR611 4.2 16.4 1.0 O1B A:TTP113 4.3 71.1 1.0 C A:ASP610 4.3 17.2 1.0 N A:SER612 4.4 17.0 1.0 O5' A:TTP113 4.4 56.6 1.0 C5' A:TTP113 4.4 48.5 1.0 CG2 A:ILE614 4.4 16.8 1.0 N A:GLN613 4.4 16.7 1.0 CB A:ASP610 4.5 18.3 1.0 CB A:ASP785 4.5 16.4 1.0 CA A:SER612 4.5 17.1 1.0 N A:ILE614 4.6 17.3 1.0 CB A:TYR611 4.7 16.5 1.0 O A:ASP610 4.7 17.8 1.0 CB A:ILE614 4.7 16.9 1.0 C A:SER612 4.7 16.8 1.0 O A:ASP785 4.7 16.3 1.0 O1A A:TTP113 4.8 60.9 1.0 CA A:ASP610 4.9 17.8 1.0

Magnesium binding site 2 out of 2 in the Ddttp-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 Ddttp-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:27.1 occ:1.00 OD1 A:ASP785 2.3 16.4 1.0 O A:HOH3055 2.4 14.0 1.0 O2A A:TTP113 2.4 60.5 1.0 O A:HOH3008 2.5 15.2 1.0 OD1 A:ASP610 2.6 18.9 1.0 CG A:ASP610 3.3 18.4 1.0 CG A:ASP785 3.4 16.9 1.0 PA A:TTP113 3.4 60.1 1.0 C3' B:2DT112 3.4 16.1 1.0 OD2 A:ASP610 3.5 19.9 1.0 OD2 A:ASP785 3.7 16.6 1.0 MG A:MG1001 3.7 2.0 1.0 O1A A:TTP113 3.8 60.9 1.0 O5' A:TTP113 3.9 56.6 1.0 O1G A:TTP113 3.9 76.3 1.0 C4' B:2DT112 4.0 16.8 1.0 OE2 A:GLU786 4.1 19.5 1.0 C5' B:2DT112 4.1 17.4 1.0 CB A:GLU786 4.1 17.3 1.0 NZ A:LYS831 4.2 28.9 1.0 C5' A:TTP113 4.3 48.5 1.0 O A:VAL783 4.4 16.3 1.0 C A:ASP785 4.6 16.4 1.0 CB A:ASP610 4.6 18.3 1.0 C2' B:2DT112 4.6 15.8 1.0 CB A:ASP785 4.7 16.4 1.0 O5' B:2DT112 4.7 18.3 1.0 O3A A:TTP113 4.7 68.0 1.0 N A:GLU786 4.7 16.6 1.0 O A:ASP785 4.7 16.3 1.0 OP1 B:2DT112 4.8 18.9 1.0 N A:ASP785 4.9 16.1 1.0 O2B A:TTP113 5.0 71.6 1.0 CA A:GLU786 5.0 16.7 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