Magnesium in PDB 3au6: Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp

All present enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp:
2.7.7.7;

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp, PDB code: 3au6 was solved by S.Nakane, R.Masui, S.Kuramitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.166, 80.166, 268.555, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 31.9

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp (pdb code 3au6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp, PDB code: 3au6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg577 b:39.9 occ:1.00 OD2 A:ASP200 1.5 78.7 1.0 O1G A:DG3576 1.6 67.4 1.0 O3A A:DG3576 2.0 65.7 1.0 CG A:ASP200 2.8 77.5 1.0 PG A:DG3576 2.8 66.9 1.0 OG A:SER188 2.9 75.6 1.0 PB A:DG3576 3.0 67.7 1.0 O1A A:DG3576 3.0 63.5 1.0 OD1 A:ASP198 3.0 70.4 1.0 PA A:DG3576 3.0 65.2 1.0 OD2 A:ASP198 3.2 71.3 1.0 O2B A:DG3576 3.2 65.4 1.0 O3B A:DG3576 3.3 66.3 1.0 O A:ASP198 3.3 74.5 1.0 CG A:ASP198 3.4 72.2 1.0 O2G A:DG3576 3.5 67.6 1.0 N A:SER188 3.5 74.2 1.0 OD1 A:ASP200 3.5 77.2 1.0 CB A:SER188 3.8 75.0 1.0 O5' A:DG3576 3.8 70.5 1.0 CB A:ASP200 3.8 77.4 1.0 O3G A:DG3576 4.0 64.5 1.0 C5' A:DG3576 4.0 76.8 1.0 MG A:MG578 4.1 0.1 1.0 CA A:GLY187 4.2 72.9 1.0 C A:ASP198 4.3 74.6 1.0 O1B A:DG3576 4.3 66.9 1.0 O2A A:DG3576 4.3 62.9 1.0 CA A:SER188 4.3 74.8 1.0 N A:ASP200 4.4 76.8 1.0 C A:GLY187 4.4 73.4 1.0 CB A:ASP198 4.7 73.6 1.0 CA A:ASP200 4.7 77.5 1.0 N A:ASP198 4.8 74.3 1.0 CA A:ASP198 4.9 74.1 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with Primer/Template Dna and Ddgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg578 b:0.1 occ:1.00 O1A A:DG3576 1.9 63.5 1.0 OD2 A:ASP198 2.3 71.3 1.0 OD1 A:ASP200 2.5 77.2 1.0 O5' A:DG3576 2.9 70.5 1.0 PA A:DG3576 3.0 65.2 1.0 OD1 A:ASP243 3.1 76.3 1.0 CG A:ASP198 3.3 72.2 1.0 CG A:ASP200 3.4 77.5 1.0 OD2 A:ASP200 3.6 78.7 1.0 C3' P:DDG7 3.8 80.6 1.0 OD1 A:ASP198 3.8 70.4 1.0 C5' A:DG3576 4.0 76.8 1.0 O3A A:DG3576 4.1 65.7 1.0 O2A A:DG3576 4.1 62.9 1.0 MG A:MG577 4.1 39.9 1.0 C2' P:DDG7 4.2 80.2 1.0 CG A:ASP243 4.3 77.1 1.0 CB A:ASP198 4.4 73.6 1.0 O1G A:DG3576 4.8 67.4 1.0 O2G A:DG3576 4.8 67.6 1.0 CB A:ASP200 4.8 77.4 1.0 CB A:ASP243 5.0 77.2 1.0

S.Nakane, H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. The Structural Basis of the Kinetic Mechanism of A Gap-Filling X-Family Dna Polymerase That Binds Mg(2+)-Dntp Before Binding to Dna. J.Mol.Biol. V. 417 179 2012.
ISSN: ISSN 0022-2836
PubMed: 22306405
DOI: 10.1016/J.JMB.2012.01.025