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Magnesium in PDB 4rq4: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MGCL2 For 30 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 30 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 30 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 30 S, PDB code: 4rq4 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) 40.59 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.160, 79.650, 55.310, 90.00, 106.35, 90.00
R / Rfree (%) 19 / 24.4

Other elements in 4rq4:

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 30 S also contains other interesting chemical elements:

Chlorine (Cl) 5 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 30 S (pdb code 4rq4). 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 30 S, PDB code: 4rq4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4rq4

Go back to Magnesium Binding Sites List in 4rq4
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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:19.4
occ:1.00
 OD1 A:ASP190 2.1 26.6 1.0
O1A A:DTP401 2.1 23.6 0.7
O A:HOH638 2.2 31.2 1.0
O1B A:DTP401 2.2 22.7 0.7
O22 A:PPV412 2.2 19.6 0.3
O2G A:DTP401 2.2 24.6 0.7
O21 A:PPV412 2.2 19.7 0.3
OD2 A:ASP192 2.3 22.2 1.0
OP1 P:DA11 2.5 22.1 0.3
PB A:DTP401 3.2 23.5 0.7
P2 A:PPV412 3.2 19.1 0.3
CG A:ASP190 3.3 26.1 1.0
CG A:ASP192 3.3 21.3 1.0
PA A:DTP401 3.3 23.0 0.7
PG A:DTP401 3.3 29.7 0.7
O3A A:DTP401 3.4 25.4 0.7
O12 A:PPV412 3.4 20.0 0.3
P1 A:PPV412 3.6 20.3 0.3
O A:ASP190 3.6 28.5 1.0
O3B A:DTP401 3.6 25.6 0.7
OD1 A:ASP192 3.6 20.1 1.0
MG A:MG403 3.7 13.0 1.0
OPP A:PPV412 3.8 19.8 0.3
O3G A:DTP401 3.8 27.9 0.7
P P:DA11 3.9 21.5 0.3
OD2 A:ASP190 3.9 26.5 1.0
N A:ASP190 4.0 26.8 1.0
C A:ASP190 4.0 25.8 1.0
C5' A:DTP401 4.1 22.6 0.7
O A:HOH501 4.2 25.9 1.0
O5' A:DTP401 4.2 23.4 0.7
O5' P:DA11 4.2 21.9 0.3
CA A:ASP190 4.4 26.5 1.0
CB A:ASP190 4.4 25.8 1.0
O31 A:PPV412 4.4 20.1 0.3
N A:SER180 4.5 25.9 1.0
CA A:GLY179 4.5 23.1 1.0
O2A A:DTP401 4.5 23.1 0.7
O32 A:PPV412 4.6 20.2 0.3
C5' P:DA11 4.6 21.4 0.3
O11 A:PPV412 4.6 19.4 0.3
O2B A:DTP401 4.6 24.2 0.7
CB A:ASP192 4.6 22.8 1.0
O1G A:DTP401 4.6 28.7 0.7
OP2 P:DA11 4.7 22.1 0.3
OG A:SER180 4.7 28.8 1.0
O P:HOH209 4.8 25.8 1.0
N A:MET191 4.8 26.1 1.0
O3' P:DC10 4.9 23.0 0.3
N A:ASP192 5.0 23.0 1.0

Magnesium binding site 2 out of 3 in 4rq4

Go back to Magnesium Binding Sites List in 4rq4
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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:13.0
occ:1.00
 OD2 A:ASP190 1.9 26.5 1.0
OP1 P:DA11 2.1 22.1 0.3
OD1 A:ASP192 2.1 20.1 1.0
O P:HOH209 2.3 25.8 1.0
OD2 A:ASP256 2.3 22.8 1.0
O3' P:DC10 2.5 28.2 0.7
O3' P:DC10 2.5 23.0 0.3
O1A A:DTP401 2.5 23.6 0.7
CG A:ASP190 2.8 26.1 1.0
P P:DA11 2.8 21.5 0.3
OD1 A:ASP190 2.9 26.6 1.0
CG A:ASP192 3.2 21.3 1.0
CG A:ASP256 3.4 24.1 1.0
C3' P:DC10 3.5 27.3 0.7
PA A:DTP401 3.6 23.0 0.7
OD2 A:ASP192 3.6 22.2 1.0
C3' P:DC10 3.7 23.8 0.3
MG A:MG402 3.7 19.4 1.0
OP2 P:DA11 3.8 22.1 0.3
O5' P:DA11 4.0 21.9 0.3
O5' A:DTP401 4.0 23.4 0.7
C4' P:DC10 4.0 24.2 0.3
O2A A:DTP401 4.1 23.1 0.7
C4' P:DC10 4.1 26.8 0.7
CB A:ASP256 4.1 23.1 1.0
C5' P:DC10 4.1 27.4 0.7
C5' P:DC10 4.2 25.1 0.3
CB A:ASP190 4.2 25.8 1.0
C5' P:DA11 4.2 21.4 0.3
C5' A:DTP401 4.2 22.6 0.7
OD1 A:ASP256 4.4 25.0 1.0
CB A:ASP192 4.5 22.8 1.0
O A:MET191 4.7 24.8 1.0
OP1 P:DC10 4.7 26.2 0.3
OP1 P:DC10 4.7 26.2 0.7
O2G A:DTP401 4.8 24.6 0.7
O5' P:DC10 4.8 26.3 0.7
C2' P:DC10 4.8 26.8 0.7
C2' P:DC10 4.8 23.8 0.3
O5' P:DC10 4.8 25.4 0.3
NH2 A:ARG254 4.9 22.2 1.0
O3A A:DTP401 5.0 25.4 0.7

Magnesium binding site 3 out of 3 in 4rq4

Go back to Magnesium Binding Sites List in 4rq4
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 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:38.2
occ:0.80
 O2A A:DTP401 1.8 23.1 0.7
O A:HOH642 2.2 38.2 0.5
O A:HOH635 2.3 36.1 1.0
OP2 P:DA11 2.3 22.1 0.3
O P:HOH210 2.5 46.0 1.0
PA A:DTP401 3.1 23.0 0.7
O3A A:DTP401 3.1 25.4 0.7
P P:DA11 3.7 21.5 0.3
O12 A:PPV412 3.9 20.0 0.3
O5' A:DTP401 4.0 23.4 0.7
O5' P:DA11 4.3 21.9 0.3
O1A A:DTP401 4.3 23.6 0.7
OP1 P:DA11 4.4 22.1 0.3
OPP A:PPV412 4.4 19.8 0.3
O P:HOH209 4.4 25.8 1.0
OP2 P:DC10 4.6 29.5 0.7
O31 A:PPV412 4.6 20.1 0.3
OP2 P:DC10 4.6 27.5 0.3
PB A:DTP401 4.6 23.5 0.7
O1G A:DTP401 4.7 28.7 0.7
O2G A:DTP401 4.7 24.6 0.7
O3' P:DC10 4.8 23.0 0.3
O P:HOH204 4.8 42.8 1.0
C8 A:DTP401 4.8 24.2 0.7
C3' P:DC10 4.9 23.8 0.3
P2 A:PPV412 4.9 19.1 0.3
O A:HOH502 4.9 24.3 1.0
C8 P:DA11 4.9 22.1 0.3
N7 P:DA11 5.0 21.8 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 03:16:36 2024

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