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Magnesium in PDB 4rpz: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp Soaked with MGCL2 For 60 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 60 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 60 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 60 S, PDB code: 4rpz was solved by R.Vyas, A.J.Reed, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.19 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.410, 79.320, 55.410, 90.00, 106.20, 90.00
R / Rfree (%) 19.5 / 25.1

Other elements in 4rpz:

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 60 S also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 4 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 60 S (pdb code 4rpz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 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 60 S, PDB code: 4rpz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4rpz

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Magnesium binding site 1 out of 3 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 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:22.4
occ:1.00
 OD1 A:ASP192 2.2 20.3 1.0
OD2 A:ASP190 2.2 25.5 1.0
O2A A:DCP410 2.2 24.0 0.2
OD2 A:ASP256 2.2 20.9 1.0
O3' P:DC10 2.2 22.2 0.2
O3' P:DC10 2.2 22.6 0.8
OP1 P:DC11 2.2 22.8 0.8
P P:DC11 2.7 22.4 0.8
CG A:ASP190 2.9 24.4 1.0
OD1 A:ASP190 3.0 25.2 1.0
CG A:ASP192 3.1 19.9 1.0
C3' P:DC10 3.3 22.2 0.2
PA A:DCP410 3.4 24.5 0.2
CG A:ASP256 3.4 20.5 1.0
OD2 A:ASP192 3.4 19.6 1.0
C3' P:DC10 3.5 22.4 0.8
MG A:MG402 3.6 24.3 1.0
O1A A:DCP410 3.8 24.6 0.2
C4' P:DC10 3.8 22.7 0.8
OP2 P:DC11 3.8 22.6 0.8
O5' P:DC11 3.9 21.4 0.8
C4' P:DC10 3.9 22.4 0.2
C5' P:DC10 4.0 22.7 0.2
CB A:ASP256 4.0 18.8 1.0
C5' P:DC10 4.0 22.9 0.8
C5' A:DCP410 4.0 23.9 0.2
O5' A:DCP410 4.1 24.2 0.2
C5' P:DC11 4.2 20.8 0.8
CB A:ASP190 4.4 23.3 1.0
OD1 A:ASP256 4.4 21.4 1.0
CB A:ASP192 4.5 19.9 1.0
C2' P:DC10 4.5 22.2 0.8
C2' P:DC10 4.6 22.1 0.2
O3A A:DCP410 4.7 24.9 0.2
O A:HOH619 4.7 24.4 0.5
OP1 P:DC10 4.7 23.1 0.2
O A:MET191 4.7 21.2 1.0
OP1 P:DC10 4.8 22.4 0.8
O5' P:DC10 4.8 23.0 0.2
O5' P:DC10 4.8 23.3 0.8
O3G A:DCP410 4.9 25.5 0.2
O31 A:PPV409 5.0 27.1 0.8
O1B A:DCP410 5.0 24.8 0.2

Magnesium binding site 2 out of 3 in 4rpz

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Magnesium binding site 2 out of 3 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 60 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 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.3
occ:1.00
 OD1 A:ASP190 2.1 25.2 1.0
O11 A:PPV409 2.2 26.1 0.8
O1B A:DCP410 2.2 24.8 0.2
O A:HOH610 2.2 24.7 1.0
O2A A:DCP410 2.2 24.0 0.2
OP1 P:DC11 2.2 22.8 0.8
O3G A:DCP410 2.2 25.5 0.2
O22 A:PPV409 2.2 28.3 0.8
OD2 A:ASP192 2.2 19.6 1.0
O3A A:DCP410 3.0 24.9 0.2
PB A:DCP410 3.0 25.1 0.2
P1 A:PPV409 3.1 27.7 0.8
PA A:DCP410 3.1 24.5 0.2
O31 A:PPV409 3.2 27.1 0.8
CG A:ASP192 3.3 19.9 1.0
CG A:ASP190 3.3 24.4 1.0
PG A:DCP410 3.4 26.3 0.2
P2 A:PPV409 3.5 31.3 0.8
O3B A:DCP410 3.5 25.5 0.2
MG A:MG401 3.6 22.4 1.0
P P:DC11 3.6 22.4 0.8
OD1 A:ASP192 3.7 20.3 1.0
OPP A:PPV409 3.7 28.9 0.8
O A:ASP190 3.9 21.7 1.0
OD2 A:ASP190 4.0 25.5 1.0
O A:HOH619 4.0 24.4 0.5
O1G A:DCP410 4.0 25.7 0.2
N A:ASP190 4.1 22.1 1.0
O A:HOH535 4.1 15.4 1.0
O5' A:DCP410 4.1 24.2 0.2
C5' A:DCP410 4.2 23.9 0.2
C A:ASP190 4.2 22.4 1.0
O5' P:DC11 4.3 21.4 0.8
C5' P:DC11 4.3 20.8 0.8
O12 A:PPV409 4.3 28.9 0.8
O1A A:DCP410 4.4 24.6 0.2
OP2 P:DC11 4.4 22.6 0.8
CB A:ASP190 4.4 23.3 1.0
CA A:ASP190 4.4 22.4 1.0
O2B A:DCP410 4.4 25.0 0.2
O21 A:PPV409 4.4 26.9 0.8
CA A:GLY179 4.6 20.2 1.0
N A:SER180 4.6 20.2 1.0
CB A:ASP192 4.6 19.9 1.0
O32 A:PPV409 4.6 30.0 0.8
O3' P:DC10 4.6 22.6 0.8
O2G A:DCP410 4.6 26.1 0.2
OG A:SER180 4.7 19.3 1.0
MG P:MG101 4.8 25.5 0.5
N A:ASP192 4.9 19.6 1.0
O3' P:DC10 5.0 22.2 0.2
N A:MET191 5.0 21.7 1.0

Magnesium binding site 3 out of 3 in 4rpz

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Magnesium binding site 3 out of 3 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 60 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:25.5
occ:0.50
 O A:HOH613 2.2 31.5 1.0
O1A A:DCP410 2.2 24.6 0.2
O3A A:DCP410 2.2 24.9 0.2
O A:HOH621 2.2 25.6 0.5
O P:HOH210 2.2 24.6 0.5
O A:HOH619 2.2 24.4 0.5
OP2 P:DC11 2.2 22.6 0.8
O31 A:PPV409 2.2 27.1 0.8
PA A:DCP410 2.6 24.5 0.2
P P:DC11 3.3 22.4 0.8
O P:HOH209 3.4 28.2 1.0
O2G A:DCP410 3.6 26.1 0.2
PB A:DCP410 3.6 25.1 0.2
O32 A:PPV409 3.6 30.0 0.8
P1 A:PPV409 3.6 27.7 0.8
O5' A:DCP410 3.6 24.2 0.2
O3G A:DCP410 3.7 25.5 0.2
OP1 P:DC11 3.8 22.8 0.8
O5' P:DC11 3.9 21.4 0.8
OPP A:PPV409 3.9 28.9 0.8
O A:HOH620 3.9 26.3 1.0
O2A A:DCP410 3.9 24.0 0.2
O3B A:DCP410 3.9 25.5 0.2
PG A:DCP410 4.0 26.3 0.2
O2B A:DCP410 4.0 25.0 0.2
O22 A:PPV409 4.1 28.3 0.8
P2 A:PPV409 4.1 31.3 0.8
O21 A:PPV409 4.4 26.9 0.8
O3' P:DC10 4.7 22.6 0.8
O11 A:PPV409 4.7 26.1 0.8
O1B A:DCP410 4.7 24.8 0.2
MG A:MG402 4.8 24.3 1.0
C5' A:DCP410 5.0 23.9 0.2

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 03:15:57 2024

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