Magnesium in PDB 1t8e: T7 Dna Polymerase Ternary Complex with Dctp at the Insertion Site.

All present enzymatic activity of T7 Dna Polymerase Ternary Complex with Dctp at the Insertion Site.:
2.7.7.7;

The structure of T7 Dna Polymerase Ternary Complex with Dctp at the Insertion Site., PDB code: 1t8e 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)	28.71 / 2.54
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.285, 218.121, 52.133, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.5

The binding sites of Magnesium atom in the T7 Dna Polymerase Ternary Complex with Dctp at the Insertion Site. (pdb code 1t8e). 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 Dctp at the Insertion Site., PDB code: 1t8e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the T7 Dna Polymerase Ternary Complex with Dctp 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 Dctp at the Insertion Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:16.7 occ:1.00 OD1 A:ASP475 2.2 26.4 1.0 O2A A:DCT1023 2.3 23.8 1.0 O1G A:DCT1023 2.3 24.5 1.0 OD2 A:ASP654 2.3 17.8 1.0 O2B A:DCT1023 2.4 25.4 1.0 O A:ALA476 2.5 20.6 1.0 O3B A:DCT1023 2.9 26.7 1.0 PB A:DCT1023 3.0 26.1 1.0 O3A A:DCT1023 3.0 26.9 1.0 CG A:ASP475 3.1 25.2 1.0 PG A:DCT1023 3.1 21.6 1.0 PA A:DCT1023 3.1 25.3 1.0 OD2 A:ASP475 3.3 27.1 1.0 CG A:ASP654 3.4 17.1 1.0 O A:HOH4158 3.6 39.6 1.0 C A:ALA476 3.7 18.8 1.0 OD1 A:ASP654 3.7 14.0 1.0 MG A:MG4002 3.9 31.6 1.0 O2G A:DCT1023 4.0 24.9 1.0 O1A A:DCT1023 4.2 21.8 1.0 O5' A:DCT1023 4.2 23.6 1.0 N A:ALA476 4.3 17.6 1.0 O3G A:DCT1023 4.3 23.0 1.0 C5' A:DCT1023 4.3 22.6 1.0 CB A:ASP475 4.4 21.6 1.0 O1B A:DCT1023 4.4 26.3 1.0 N A:GLY478 4.5 19.6 1.0 CA A:ALA476 4.5 19.0 1.0 C A:ASP475 4.6 19.9 1.0 N A:SER477 4.6 18.6 1.0 CB A:ASP654 4.7 17.9 1.0 CA A:SER477 4.7 19.2 1.0 C A:SER477 4.9 19.4 1.0 O A:ASP654 4.9 17.7 1.0 CB A:ALA476 4.9 16.9 1.0 N A:LEU479 4.9 23.9 1.0

Magnesium binding site 2 out of 3 in the T7 Dna Polymerase Ternary Complex with Dctp 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 Dctp at the Insertion Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:31.6 occ:1.00 OD2 A:ASP475 2.4 27.1 1.0 O A:HOH4011 2.4 29.7 1.0 O2A A:DCT1023 2.4 23.8 1.0 OD1 A:ASP654 2.5 14.0 1.0 O A:HOH4012 2.9 24.4 1.0 C3' C:2DT1022 3.3 21.5 1.0 CG A:ASP475 3.4 25.2 1.0 CG A:ASP654 3.5 17.1 1.0 PA A:DCT1023 3.7 25.3 1.0 OD1 A:ASP475 3.7 26.4 1.0 CE1 A:HIS704 3.8 27.9 1.0 OD2 A:ASP654 3.9 17.8 1.0 MG A:MG4001 3.9 16.7 1.0 C4' C:2DT1022 3.9 21.9 1.0 CB A:GLU655 4.0 19.2 1.0 OE2 A:GLU655 4.1 20.7 1.0 O5' A:DCT1023 4.1 23.6 1.0 C5' C:2DT1022 4.2 21.7 1.0 NE2 A:HIS704 4.2 29.1 1.0 C2' C:2DT1022 4.3 22.7 1.0 O1A A:DCT1023 4.4 21.8 1.0 C5' A:DCT1023 4.4 22.6 1.0 O A:VAL652 4.4 20.9 1.0 C A:ASP654 4.6 17.4 1.0 O5' C:2DT1022 4.6 22.2 1.0 CB A:ASP475 4.6 21.6 1.0 O A:ASP654 4.7 17.7 1.0 N A:GLU655 4.7 17.9 1.0 CB A:ASP654 4.9 17.9 1.0 CD A:GLU655 4.9 21.6 1.0 N A:ASP654 4.9 18.2 1.0 ND1 A:HIS704 4.9 29.9 1.0 CA A:GLU655 4.9 18.4 1.0 O3A A:DCT1023 5.0 26.9 1.0

Magnesium binding site 3 out of 3 in the T7 Dna Polymerase Ternary Complex with Dctp 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 Dctp at the Insertion Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4003 b:22.1 occ:1.00 O A:HOH4016 2.2 14.3 1.0 O A:HOH4017 2.3 40.2 1.0 O A:HOH4015 2.4 17.6 1.0 O A:HOH4013 2.4 23.8 1.0 OD1 A:ASP5 2.5 24.8 1.0 O A:HOH4014 2.5 20.9 1.0 CG A:ASP5 3.5 25.6 1.0 O A:HOH4018 3.6 27.7 1.0 OD2 A:ASP5 3.9 25.6 1.0 OD1 A:ASP65 4.1 30.1 1.0 O A:HOH4276 4.2 44.5 1.0 O A:HIS59 4.3 18.3 1.0 O A:ILE6 4.4 22.8 1.0 OD2 A:ASP65 4.4 29.6 1.0 OD1 A:ASP174 4.5 36.0 1.0 O A:HOH4020 4.5 17.4 1.0 CE A:MET107 4.5 38.0 1.0 O A:HOH4019 4.6 20.7 1.0 CG A:ASP65 4.7 27.8 1.0 CB A:ASP5 4.9 23.5 1.0 CD2 A:TYR64 5.0 17.2 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