Magnesium in PDB 1tkd: T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Dcmp at the Elongation Site

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

The structure of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Dcmp at the Elongation Site, PDB code: 1tkd 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)	47.91 / 2.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.514, 215.112, 52.035, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.5

The binding sites of Magnesium atom in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Dcmp at the Elongation Site (pdb code 1tkd). 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 Dcmp at the Elongation Site, PDB code: 1tkd:
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 Dcmp at the Elongation 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 Dcmp at the Elongation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:24.3 occ:1.00 O1G A:D3T823 1.9 30.5 1.0 O2B A:D3T823 2.1 28.7 1.0 OD2 A:ASP654 2.1 24.9 1.0 OD1 A:ASP475 2.1 39.8 1.0 O2A A:D3T823 2.3 24.6 1.0 O A:ALA476 2.5 19.7 1.0 MG A:MG902 3.0 37.5 1.0 CG A:ASP475 3.1 33.9 1.0 PG A:D3T823 3.1 30.4 1.0 CG A:ASP654 3.2 23.4 1.0 PB A:D3T823 3.2 27.2 1.0 OD2 A:ASP475 3.4 36.4 1.0 O3B A:D3T823 3.5 29.2 1.0 PA A:D3T823 3.6 27.7 1.0 C A:ALA476 3.7 19.5 1.0 OD1 A:ASP654 3.7 22.1 1.0 O3A A:D3T823 3.8 27.6 1.0 O A:HOH1608 3.9 39.0 1.0 O2G A:D3T823 4.0 27.8 1.0 O3G A:D3T823 4.2 27.1 1.0 N A:ALA476 4.3 20.2 1.0 N A:GLY478 4.3 16.3 1.0 CB A:ASP654 4.4 18.6 1.0 C5' A:D3T823 4.5 28.7 1.0 CB A:ASP475 4.5 27.4 1.0 CA A:ALA476 4.5 20.2 1.0 O5' A:D3T823 4.5 29.2 1.0 O1B A:D3T823 4.6 27.9 1.0 N A:SER477 4.6 18.5 1.0 O1A A:D3T823 4.7 24.2 1.0 C A:ASP475 4.7 23.3 1.0 CA A:SER477 4.7 18.6 1.0 O A:HOH1372 4.8 20.2 1.0 C A:SER477 4.8 16.9 1.0 O A:ASP654 4.9 15.7 1.0 N A:LEU479 4.9 19.9 1.0 CB A:ALA476 4.9 18.4 1.0

Magnesium binding site 2 out of 3 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Dcmp at the Elongation 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 Dcmp at the Elongation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:37.5 occ:1.00 OD2 A:ASP475 2.0 36.4 1.0 O2A A:D3T823 2.3 24.6 1.0 O A:HOH1372 2.5 20.2 1.0 OD1 A:ASP654 2.5 22.1 1.0 O A:HOH1507 2.7 20.5 1.0 CG A:ASP475 2.9 33.9 1.0 MG A:MG901 3.0 24.3 1.0 OD2 A:ASP654 3.1 24.9 1.0 CG A:ASP654 3.1 23.4 1.0 OD1 A:ASP475 3.2 39.8 1.0 O A:HOH1608 3.4 39.0 1.0 PA A:D3T823 3.5 27.7 1.0 O1G A:D3T823 3.8 30.5 1.0 C3' P:DOC822 3.9 14.7 1.0 O1A A:D3T823 4.0 24.2 1.0 CE1 A:HIS704 4.1 34.6 1.0 CB A:ASP475 4.3 27.4 1.0 O5' A:D3T823 4.3 29.2 1.0 CB A:GLU655 4.5 16.9 1.0 O2B A:D3T823 4.5 28.7 1.0 C5' A:D3T823 4.6 28.7 1.0 CB A:ASP654 4.6 18.6 1.0 C4' P:DOC822 4.7 15.4 1.0 C5' P:DOC822 4.7 12.1 1.0 O A:ASP654 4.7 15.7 1.0 NE2 A:HIS704 4.7 33.2 1.0 C A:ASP654 4.7 15.6 1.0 OE2 A:GLU655 4.8 24.6 1.0 O3A A:D3T823 4.8 27.6 1.0

Magnesium binding site 3 out of 3 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Dcmp at the Elongation 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 Dcmp at the Elongation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:18.6 occ:1.00 OD1 A:ASP5 2.2 18.3 1.0 O A:HOH1094 2.2 14.8 1.0 O A:HOH1093 2.2 15.0 1.0 O A:HOH1091 2.2 15.5 1.0 O A:HOH1479 2.2 20.0 1.0 O A:HOH1480 2.3 39.2 1.0 CG A:ASP5 3.2 18.6 1.0 OD2 A:ASP5 3.6 17.7 1.0 O A:HOH1096 4.0 21.4 1.0 O A:HOH1095 4.1 59.3 1.0 OD1 A:ASP65 4.1 13.6 1.0 O A:ILE6 4.1 19.2 1.0 OD2 A:ASP65 4.2 12.9 1.0 O A:HOH1030 4.2 14.5 1.0 O A:HIS59 4.3 13.0 1.0 O A:HOH1092 4.4 24.4 1.0 O A:HOH1090 4.4 22.3 1.0 OD2 A:ASP174 4.5 28.0 1.0 CB A:ASP5 4.5 16.0 1.0 CG A:ASP65 4.6 13.8 1.0 CE A:MET107 4.7 22.1 1.0 N A:ILE6 4.8 16.3 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