Atomistry » Magnesium » PDB 4rkf-4rrh » 4rq6
Atomistry »
  Magnesium »
    PDB 4rkf-4rrh »
      4rq6 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy