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Magnesium in PDB 4rq6: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S

Enzymatic activity of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S

All present enzymatic activity of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S, PDB code: 4rq6 was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.410, 80.450, 55.680, 90.00, 107.75, 90.00
R / Rfree (%) 19.8 / 25.2

Other elements in 4rq6:

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S (pdb code 4rq6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S, PDB code: 4rq6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4rq6

Go back to Magnesium Binding Sites List in 4rq6
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:28.9
occ:1.00
 OP1 P:DA11 2.2 28.7 1.0
O32 A:PPV401 2.2 32.6 1.0
OD1 A:ASP190 2.2 32.9 1.0
OD2 A:ASP192 2.2 28.6 1.0
O A:HOH505 2.2 26.1 1.0
O21 A:PPV401 2.2 36.8 1.0
P2 A:PPV401 3.2 31.9 1.0
CG A:ASP192 3.3 27.7 1.0
CG A:ASP190 3.3 33.2 1.0
O12 A:PPV401 3.4 36.5 1.0
NA A:NA403 3.5 28.6 1.0
P P:DA11 3.5 31.3 1.0
P1 A:PPV401 3.5 40.0 1.0
OPP A:PPV401 3.7 35.7 1.0
OD1 A:ASP192 3.7 29.3 1.0
OD2 A:ASP190 3.9 36.8 1.0
O A:ASP190 4.0 28.8 1.0
O P:HOH205 4.1 39.1 1.0
O5' P:DA11 4.1 28.7 1.0
O A:HOH538 4.2 14.3 0.5
C5' P:DA11 4.3 28.2 1.0
N A:ASP190 4.3 27.8 1.0
C A:ASP190 4.3 28.1 1.0
OP2 P:DA11 4.4 28.6 1.0
O31 A:PPV401 4.4 36.9 1.0
O22 A:PPV401 4.5 34.9 1.0
CB A:ASP192 4.5 28.5 1.0
CB A:ASP190 4.6 31.2 1.0
O11 A:PPV401 4.6 37.1 1.0
O3' P:DC10 4.6 32.3 1.0
CA A:ASP190 4.6 28.6 1.0
CA A:GLY179 4.6 30.7 1.0
N A:SER180 4.6 31.6 1.0
MG P:MG101 4.6 36.7 0.8
OG A:SER180 4.7 33.8 1.0
N A:ASP192 5.0 27.3 1.0

Magnesium binding site 2 out of 2 in 4rq6

Go back to Magnesium Binding Sites List in 4rq6
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:36.7
occ:0.80
 O P:HOH207 2.2 34.7 0.5
O A:HOH554 2.2 37.3 0.5
OP2 P:DA11 2.2 28.6 1.0
O12 A:PPV401 2.2 36.5 1.0
O P:HOH205 2.2 39.1 1.0
O A:HOH525 2.2 38.5 1.0
P P:DA11 3.3 31.3 1.0
O11 A:PPV401 3.5 37.1 1.0
P2 A:PPV401 3.6 31.9 1.0
OP1 P:DA11 3.8 28.7 1.0
O5' P:DA11 4.0 28.7 1.0
O21 A:PPV401 4.0 36.8 1.0
OPP A:PPV401 4.0 35.7 1.0
P1 A:PPV401 4.1 40.0 1.0
O A:HOH552 4.4 32.9 1.0
O32 A:PPV401 4.6 32.6 1.0
O22 A:PPV401 4.6 34.9 1.0
O3' P:DC10 4.6 32.3 1.0
MG A:MG402 4.6 28.9 1.0

Reference:

R.Vyas, A.J.Reed, E.J.Tokarsky, Z.Suo. Viewing Human Dna Polymerase Beta Faithfully and Unfaithfully Bypass An Oxidative Lesion By Time-Dependent Crystallography. J.Am.Chem.Soc. V. 137 5225 2015.
ISSN: ISSN 0002-7863
PubMed: 25825995
DOI: 10.1021/JACS.5B02109
Page generated: Tue Aug 20 03:16:48 2024

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