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Magnesium in PDB 4rq5: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp 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 Datp 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 Datp 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 Datp Soaked with MGCL2 For 60 S, PDB code: 4rq5 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) 50.00 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.212, 79.702, 55.384, 90.00, 106.66, 90.00
R / Rfree (%) 19.6 / 26.6

Other elements in 4rq5:

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 60 S also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 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 60 S (pdb code 4rq5). 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 Datp Soaked with MGCL2 For 60 S, PDB code: 4rq5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4rq5

Go back to Magnesium Binding Sites List in 4rq5
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 Datp 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 Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:26.4
occ:1.00
 OD2 A:ASP190 2.2 29.3 1.0
OD2 A:ASP256 2.2 25.6 1.0
OD1 A:ASP192 2.2 27.8 1.0
O A:HOH546 2.2 29.5 1.0
O3' P:DC10 2.2 28.9 0.7
O3' P:DC10 2.2 27.8 0.3
O2A A:DTP410 2.2 27.8 0.3
OP1 P:DA11 2.5 27.6 0.7
P P:DA11 2.9 29.2 0.7
CG A:ASP190 3.0 31.6 1.0
OD1 A:ASP190 3.1 32.1 1.0
CG A:ASP192 3.2 27.1 1.0
PA A:DTP410 3.3 28.4 0.3
C3' P:DC10 3.3 29.0 0.3
CG A:ASP256 3.4 25.5 1.0
C3' P:DC10 3.4 31.0 0.7
OD2 A:ASP192 3.6 26.6 1.0
O1A A:DTP410 3.6 30.6 0.3
MG A:MG402 3.6 27.7 1.0
C5' A:DTP410 3.8 27.7 0.3
C4' P:DC10 3.8 33.0 0.7
O5' A:DTP410 3.9 28.4 0.3
OP2 P:DA11 4.0 31.0 0.7
O5' P:DA11 4.0 27.9 0.7
CB A:ASP256 4.0 25.0 1.0
C4' P:DC10 4.0 29.9 0.3
C5' P:DC10 4.1 33.8 0.7
C5' P:DC10 4.1 30.6 0.3
C5' P:DA11 4.1 26.8 0.7
OD1 A:ASP256 4.3 25.1 1.0
CB A:ASP190 4.4 30.0 1.0
C2' P:DC10 4.5 31.1 0.7
OP1 P:DC10 4.5 32.1 0.3
CB A:ASP192 4.5 27.0 1.0
C2' P:DC10 4.6 29.0 0.3
O5' P:DC10 4.7 35.5 0.7
O2G A:DTP410 4.7 29.8 0.3
O3A A:DTP410 4.7 29.6 0.3
O5' P:DC10 4.7 32.0 0.3
NH2 A:ARG254 4.7 27.0 1.0
O A:MET191 4.7 32.8 1.0
OP1 P:DC10 4.9 33.6 0.7

Magnesium binding site 2 out of 3 in 4rq5

Go back to Magnesium Binding Sites List in 4rq5
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 Datp 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 Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.7
occ:1.00
 O2A A:DTP410 1.9 27.8 0.3
OP1 P:DA11 2.2 27.6 0.7
OD1 A:ASP190 2.2 32.1 1.0
O12 A:PPV409 2.2 30.4 0.7
O2G A:DTP410 2.2 29.8 0.3
O A:HOH547 2.2 25.3 1.0
O2B A:DTP410 2.2 29.3 0.3
OD2 A:ASP192 2.2 26.6 1.0
O21 A:PPV409 2.2 29.3 0.7
PA A:DTP410 2.9 28.4 0.3
O3A A:DTP410 3.0 29.6 0.3
PB A:DTP410 3.0 30.0 0.3
CG A:ASP192 3.2 27.1 1.0
PG A:DTP410 3.2 31.9 0.3
P1 A:PPV409 3.2 30.7 0.7
CG A:ASP190 3.3 31.6 1.0
O11 A:PPV409 3.4 29.6 0.7
O1G A:DTP410 3.5 31.1 0.3
P2 A:PPV409 3.5 34.7 0.7
OD1 A:ASP192 3.6 27.8 1.0
O3B A:DTP410 3.6 30.7 0.3
MG A:MG401 3.6 26.4 1.0
P P:DA11 3.6 29.2 0.7
OPP A:PPV409 3.8 31.7 0.7
O5' A:DTP410 3.8 28.4 0.3
OD2 A:ASP190 3.9 29.3 1.0
O A:ASP190 3.9 29.4 1.0
N A:ASP190 4.1 28.3 1.0
C5' A:DTP410 4.1 27.7 0.3
O1A A:DTP410 4.2 30.6 0.3
C A:ASP190 4.2 30.4 1.0
O5' P:DA11 4.3 27.9 0.7
O22 A:PPV409 4.3 31.6 0.7
OG A:SER180 4.3 26.4 1.0
C5' P:DA11 4.4 26.8 0.7
O1B A:DTP410 4.4 30.5 0.3
CB A:ASP190 4.5 30.0 1.0
CA A:ASP190 4.5 29.8 1.0
OP2 P:DA11 4.5 31.0 0.7
CB A:ASP192 4.5 27.0 1.0
O3' P:DC10 4.5 28.9 0.7
O31 A:PPV409 4.6 30.9 0.7
O A:HOH546 4.6 29.5 1.0
O3G A:DTP410 4.6 33.1 0.3
O32 A:PPV409 4.6 36.9 0.7
CA A:GLY179 4.6 24.0 1.0
MG P:MG101 4.7 32.7 0.8
N A:SER180 4.7 24.3 1.0
N A:MET191 4.9 30.5 1.0

Magnesium binding site 3 out of 3 in 4rq5

Go back to Magnesium Binding Sites List in 4rq5
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 Datp 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 Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:32.7
occ:0.80
 O1A A:DTP410 2.2 30.6 0.3
OP2 P:DA11 2.2 31.0 0.7
O P:HOH202 2.2 37.0 1.0
O3A A:DTP410 2.2 29.6 0.3
O A:HOH559 2.2 36.0 1.0
O11 A:PPV409 2.2 29.6 0.7
PA A:DTP410 2.7 28.4 0.3
O2G A:DTP410 3.2 29.8 0.3
P P:DA11 3.2 29.2 0.7
OP1 P:DA11 3.5 27.6 0.7
O32 A:PPV409 3.5 36.9 0.7
P1 A:PPV409 3.6 30.7 0.7
O3G A:DTP410 3.6 33.1 0.3
PB A:DTP410 3.6 30.0 0.3
OPP A:PPV409 3.7 31.7 0.7
O5' A:DTP410 3.8 28.4 0.3
PG A:DTP410 3.8 31.9 0.3
O3B A:DTP410 3.8 30.7 0.3
O2A A:DTP410 3.9 27.8 0.3
O12 A:PPV409 3.9 30.4 0.7
P2 A:PPV409 4.0 34.7 0.7
O5' P:DA11 4.1 27.9 0.7
O1B A:DTP410 4.2 30.5 0.3
O A:HOH558 4.4 29.8 1.0
O A:HOH546 4.5 29.5 1.0
O3' P:DC10 4.5 28.9 0.7
O31 A:PPV409 4.6 30.9 0.7
O21 A:PPV409 4.6 29.3 0.7
MG A:MG402 4.7 27.7 1.0
O P:HOH203 4.7 34.5 1.0
O2B A:DTP410 4.8 29.3 0.3

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 03:16:45 2024

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