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Magnesium in PDB 4rq0: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MGCL2 For 80 S, PDB code: 4rq0 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) 44.18 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.610, 79.540, 55.460, 90.00, 106.68, 90.00
R / Rfree (%) 20.8 / 26.8

Other elements in 4rq0:

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

Chlorine (Cl) 2 atoms
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 Dctp Soaked with MGCL2 For 80 S (pdb code 4rq0). 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 Dctp Soaked with MGCL2 For 80 S, PDB code: 4rq0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4rq0

Go back to Magnesium Binding Sites List in 4rq0
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 Dctp 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 Dctp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:23.0
occ:1.00
 OP1 P:DC11 2.2 22.8 1.0
OD1 A:ASP190 2.2 23.1 1.0
O A:HOH508 2.2 20.0 1.0
O32 A:PPV401 2.2 26.2 1.0
O11 A:PPV401 2.2 27.4 1.0
OD2 A:ASP192 2.2 19.7 1.0
P2 A:PPV401 3.1 28.1 1.0
O12 A:PPV401 3.1 29.2 1.0
CG A:ASP190 3.2 22.3 1.0
CG A:ASP192 3.2 19.6 1.0
P1 A:PPV401 3.4 33.3 1.0
P P:DC11 3.5 23.6 1.0
OD1 A:ASP192 3.6 20.0 1.0
OPP A:PPV401 3.6 29.9 1.0
OD2 A:ASP190 3.6 22.8 1.0
NA A:NA404 3.7 22.1 1.0
O5' P:DC11 4.0 22.0 1.0
O A:ASP190 4.0 20.0 1.0
O31 A:PPV401 4.1 28.3 1.0
C5' P:DC11 4.2 20.3 1.0
O A:HOH507 4.2 18.2 1.0
O P:HOH202 4.2 30.4 1.0
N A:ASP190 4.2 20.9 1.0
C A:ASP190 4.3 20.6 1.0
OP2 P:DC11 4.4 23.8 1.0
O22 A:PPV401 4.4 28.3 1.0
CB A:ASP190 4.4 21.4 1.0
CA A:GLY179 4.5 22.2 1.0
N A:SER180 4.6 23.2 1.0
CA A:ASP190 4.6 20.9 1.0
O3' P:DC10 4.6 23.6 1.0
MG P:MG101 4.6 30.6 1.0
CB A:ASP192 4.6 19.7 1.0
O21 A:PPV401 4.6 33.1 1.0
O A:HOH576 4.7 32.8 1.0
OG A:SER180 4.8 23.5 1.0
N A:ASP192 5.0 18.8 1.0

Magnesium binding site 2 out of 2 in 4rq0

Go back to Magnesium Binding Sites List in 4rq0
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 Dctp 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 Dctp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:30.6
occ:1.00
 O P:HOH203 2.2 29.4 1.0
OP2 P:DC11 2.2 23.8 1.0
O P:HOH202 2.2 30.4 1.0
O12 A:PPV401 2.2 29.2 1.0
O P:HOH205 2.2 31.0 1.0
O A:HOH521 2.2 30.2 1.0
P P:DC11 3.2 23.6 1.0
O5' P:DC11 3.6 22.0 1.0
P2 A:PPV401 3.6 28.1 1.0
OP1 P:DC11 3.6 22.8 1.0
O A:HOH545 3.8 20.5 1.0
O21 A:PPV401 3.8 33.1 1.0
O11 A:PPV401 3.8 27.4 1.0
O A:HOH578 3.9 26.8 1.0
O P:HOH204 3.9 22.2 1.0
OPP A:PPV401 3.9 29.9 1.0
P1 A:PPV401 4.1 33.3 1.0
O22 A:PPV401 4.3 28.3 1.0
O3' P:DC10 4.6 23.6 1.0
MG A:MG403 4.6 23.0 1.0
O32 A:PPV401 4.7 26.2 1.0
O A:HOH576 4.8 32.8 1.0
C6 P:DC11 4.9 19.7 1.0
C5' P:DC11 4.9 20.3 1.0
C5 P:DC11 5.0 19.7 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 03:16:01 2024

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