Magnesium in PDB 1tk0: T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site

All present enzymatic activity of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site:
2.7.7.7;

The structure of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site, PDB code: 1tk0 was solved by L.G.Brieba, B.F.Eichman, R.J.Kokoska, S.Doublie, T.A.Kunkel, T.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.85 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.230, 215.096, 52.136, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.3

The binding sites of Magnesium atom in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site (pdb code 1tk0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site, PDB code: 1tk0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg991 b:42.1 occ:1.00 OD1 A:ASP475 2.0 37.5 1.0 O2B A:DCT823 2.1 36.7 1.0 O1G A:DCT823 2.1 36.9 1.0 OD2 A:ASP654 2.1 30.5 1.0 O A:ALA476 2.1 26.8 1.0 O2A A:DCT823 2.3 35.1 1.0 CG A:ASP475 3.1 33.1 1.0 CG A:ASP654 3.2 28.5 1.0 PB A:DCT823 3.2 35.4 1.0 PG A:DCT823 3.2 39.1 1.0 C A:ALA476 3.3 26.1 1.0 PA A:DCT823 3.5 36.2 1.0 MG A:MG992 3.5 33.7 1.0 O3B A:DCT823 3.5 37.3 1.0 OD2 A:ASP475 3.6 36.7 1.0 O3A A:DCT823 3.7 37.5 1.0 OD1 A:ASP654 3.7 28.8 1.0 O A:HOH1433 3.8 41.8 1.0 N A:ALA476 3.9 23.9 1.0 O2G A:DCT823 4.0 37.6 1.0 O A:HOH1249 4.0 39.8 1.0 CA A:ALA476 4.1 26.2 1.0 CB A:ASP475 4.3 28.7 1.0 N A:SER477 4.3 26.0 1.0 C5' A:DCT823 4.3 35.8 1.0 C A:ASP475 4.3 25.8 1.0 CB A:ASP654 4.4 26.4 1.0 N A:GLY478 4.4 25.5 1.0 O3G A:DCT823 4.4 39.8 1.0 O5' A:DCT823 4.5 36.8 1.0 CA A:SER477 4.5 26.2 1.0 CB A:ALA476 4.5 24.5 1.0 O A:ASP654 4.5 23.1 1.0 O1B A:DCT823 4.6 36.5 1.0 O1A A:DCT823 4.6 34.7 1.0 N A:LEU479 4.7 27.2 1.0 C A:SER477 4.7 24.6 1.0 CA A:ASP475 4.8 25.9 1.0 O A:ASP475 4.9 26.1 1.0 CB A:LEU479 4.9 29.8 1.0

Magnesium binding site 2 out of 3 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg992 b:33.7 occ:1.00 OD2 A:ASP475 2.1 36.7 1.0 OD1 A:ASP654 2.2 28.8 1.0 O2A A:DCT823 2.4 35.1 1.0 O A:HOH1618 2.5 35.1 1.0 O A:HOH1333 2.5 30.2 1.0 CG A:ASP475 3.0 33.1 1.0 CG A:ASP654 3.1 28.5 1.0 OD1 A:ASP475 3.2 37.5 1.0 OD2 A:ASP654 3.3 30.5 1.0 PA A:DCT823 3.5 36.2 1.0 MG A:MG991 3.5 42.1 1.0 C3' P:DDG822 3.5 27.6 1.0 O A:HOH1249 3.8 39.8 1.0 O1A A:DCT823 3.9 34.7 1.0 O5' A:DCT823 3.9 36.8 1.0 CE1 A:HIS704 4.0 42.1 1.0 C5' A:DCT823 4.1 35.8 1.0 OE2 A:GLU655 4.2 32.3 1.0 CB A:GLU655 4.2 25.8 1.0 C4' P:DDG822 4.3 26.2 1.0 O A:ASP654 4.4 23.1 1.0 C A:ASP654 4.4 25.1 1.0 O1G A:DCT823 4.4 36.9 1.0 CB A:ASP654 4.4 26.4 1.0 CB A:ASP475 4.4 28.7 1.0 NE2 A:HIS704 4.5 41.9 1.0 O A:VAL652 4.6 21.2 1.0 C2' P:DDG822 4.6 26.9 1.0 C5' P:DDG822 4.6 24.9 1.0 N A:ASP654 4.7 22.1 1.0 N A:GLU655 4.7 25.0 1.0 CA A:ASP654 4.7 24.9 1.0 O3A A:DCT823 4.9 37.5 1.0 CD A:GLU655 4.9 30.1 1.0 O5' P:DDG822 4.9 26.2 1.0 O2B A:DCT823 4.9 36.7 1.0 CG A:GLU655 4.9 31.3 1.0

Magnesium binding site 3 out of 3 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Ddctp at the Insertion Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg993 b:29.8 occ:1.00 OD1 A:ASP5 2.1 20.1 1.0 O A:HOH1622 2.1 19.1 1.0 O A:HOH1621 2.2 28.1 1.0 O A:HOH1054 2.2 24.8 1.0 O A:HOH1113 2.3 25.4 1.0 O A:HOH1620 2.3 29.3 1.0 CG A:ASP5 3.1 23.2 1.0 OD2 A:ASP5 3.3 25.6 1.0 O A:ILE6 4.0 24.6 1.0 OD2 A:ASP65 4.1 20.3 1.0 OD2 A:ASP174 4.1 36.8 1.0 O A:HOH1008 4.2 23.0 1.0 O A:HOH1161 4.2 24.9 1.0 OD1 A:ASP65 4.3 19.0 1.0 O A:HOH1105 4.3 29.3 1.0 O A:HOH1415 4.4 38.0 1.0 O A:HIS59 4.4 18.6 1.0 CB A:ASP5 4.4 21.7 1.0 CG A:ASP65 4.6 20.2 1.0 N A:ILE6 4.8 22.1 1.0 CE A:MET107 5.0 32.4 1.0 CA A:ASP5 5.0 22.9 1.0

L.G.Brieba, B.F.Eichman, R.J.Kokoska, S.Doublie, T.A.Kunkel, T.Ellenberger. Structural Basis For the Dual Coding Potential of 8-Oxoguanosine By A High-Fidelity Dna Polymerase. Embo J. V. 23 3452 2004.
ISSN: ISSN 0261-4189
PubMed: 15297882
DOI: 10.1038/SJ.EMBOJ.7600354