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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3au6:

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

Magnesium Binding Sites:

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 3au6

Go back to Magnesium Binding Sites List in 3au6
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 3au6

Go back to Magnesium Binding Sites List in 3au6
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

Reference:

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
Page generated: Mon Dec 14 07:54:14 2020

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