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Magnesium in PDB 4rpy: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MGCL2 For 30 S, PDB code: 4rpy 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) 31.23 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.440, 79.530, 55.520, 90.00, 106.61, 90.00
R / Rfree (%) 19 / 23

Other elements in 4rpy:

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 30 S also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 7 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 30 S (pdb code 4rpy). 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 30 S, PDB code: 4rpy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4rpy

Go back to Magnesium Binding Sites List in 4rpy
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 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 Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:11.3
occ:1.00
 OD2 A:ASP190 2.0 20.5 1.0
OD1 A:ASP192 2.1 15.7 1.0
O2A A:DCP414 2.2 14.5 0.5
OD2 A:ASP256 2.2 15.1 1.0
OP1 P:DC11 2.2 16.8 0.5
O3' P:DC10 2.4 18.2 0.5
O P:HOH201 2.4 34.7 1.0
O3' P:DC10 2.4 17.8 0.5
CG A:ASP190 2.8 18.1 1.0
P P:DC11 2.9 17.1 0.5
OD1 A:ASP190 2.9 17.3 1.0
CG A:ASP192 3.1 15.3 1.0
CG A:ASP256 3.4 14.9 1.0
PA A:DCP414 3.4 15.7 0.5
OD2 A:ASP192 3.5 15.9 1.0
MG A:MG402 3.6 14.4 1.0
C3' P:DC10 3.6 17.6 0.5
C3' P:DC10 3.7 17.7 0.5
OP2 P:DC11 3.9 17.8 0.5
O1A A:DCP414 3.9 16.5 0.5
CB A:ASP256 4.0 14.1 1.0
C4' P:DC10 4.0 17.9 0.5
O5' A:DCP414 4.0 14.3 0.5
O5' P:DC11 4.1 16.2 0.5
C4' P:DC10 4.1 17.6 0.5
O A:HOH698 4.1 39.0 1.0
C5' P:DC10 4.1 17.9 0.5
C5' P:DC10 4.2 18.2 0.5
CB A:ASP190 4.2 17.1 1.0
C5' P:DC11 4.3 15.6 0.5
C5' A:DCP414 4.3 13.6 0.5
OD1 A:ASP256 4.4 15.4 1.0
CB A:ASP192 4.5 14.9 1.0
O3G A:DCP414 4.6 16.4 0.5
O A:MET191 4.7 15.1 1.0
O A:HOH704 4.7 35.6 1.0
OP1 P:DC10 4.8 18.7 0.5
C2' P:DC10 4.8 17.7 0.5
OP1 P:DC10 4.8 18.8 0.5
O3A A:DCP414 4.8 16.1 0.5
O5' P:DC10 4.9 18.4 0.5
C2' P:DC10 4.9 17.4 0.5
O5' P:DC10 4.9 18.5 0.5
C A:MET191 4.9 15.9 1.0
NH2 A:ARG254 5.0 14.4 1.0
CA A:ASP192 5.0 14.5 1.0

Magnesium binding site 2 out of 3 in 4rpy

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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 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 Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.4
occ:1.00
 O2B A:DCP414 2.0 15.3 0.5
O2A A:DCP414 2.1 14.5 0.5
O3G A:DCP414 2.1 16.4 0.5
OD1 A:ASP190 2.2 17.3 1.0
O A:HOH501 2.2 15.7 1.0
OP1 P:DC11 2.2 16.8 0.5
O21 A:PPV413 2.2 14.7 0.5
O12 A:PPV413 2.2 15.3 0.5
OD2 A:ASP192 2.3 15.9 1.0
PB A:DCP414 3.0 15.9 0.5
PA A:DCP414 3.1 15.7 0.5
O3A A:DCP414 3.2 16.1 0.5
P1 A:PPV413 3.3 15.6 0.5
CG A:ASP192 3.3 15.3 1.0
PG A:DCP414 3.3 17.6 0.5
CG A:ASP190 3.3 18.1 1.0
O11 A:PPV413 3.4 16.4 0.5
O3B A:DCP414 3.5 16.3 0.5
MG A:MG401 3.6 11.3 1.0
P P:DC11 3.6 17.1 0.5
OD1 A:ASP192 3.6 15.7 1.0
P2 A:PPV413 3.7 16.4 0.5
O A:ASP190 3.8 16.4 1.0
O1G A:DCP414 3.9 16.9 0.5
OD2 A:ASP190 3.9 20.5 1.0
OPP A:PPV413 4.0 15.6 0.5
C5' A:DCP414 4.0 13.6 0.5
O5' A:DCP414 4.1 14.3 0.5
N A:ASP190 4.2 16.9 1.0
C A:ASP190 4.2 17.1 1.0
O5' P:DC11 4.2 16.2 0.5
O A:HOH704 4.3 35.6 1.0
O A:HOH502 4.3 16.7 1.0
C5' P:DC11 4.3 15.6 0.5
OP2 P:DC11 4.4 17.8 0.5
O1B A:DCP414 4.4 15.8 0.5
O1A A:DCP414 4.4 16.5 0.5
CB A:ASP190 4.5 17.1 1.0
CA A:ASP190 4.5 16.9 1.0
O32 A:PPV413 4.5 16.0 0.5
CA A:GLY179 4.5 14.7 1.0
O31 A:PPV413 4.6 15.4 0.5
N A:SER180 4.6 14.9 1.0
O P:HOH201 4.6 34.7 1.0
O2G A:DCP414 4.6 17.4 0.5
CB A:ASP192 4.6 14.9 1.0
O3' P:DC10 4.7 17.8 0.5
O22 A:PPV413 4.7 15.5 0.5
MG P:MG101 4.8 17.5 0.5
OG A:SER180 4.8 15.5 1.0
O3' P:DC10 4.9 18.2 0.5
N A:ASP192 5.0 14.7 1.0
N A:MET191 5.0 16.7 1.0

Magnesium binding site 3 out of 3 in 4rpy

Go back to Magnesium Binding Sites List in 4rpy
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 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 Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:17.5
occ:0.50
 O1A A:DCP414 2.2 16.5 0.5
O A:HOH703 2.2 17.8 0.5
O A:HOH702 2.2 17.8 0.5
O A:HOH701 2.2 19.6 1.0
O3A A:DCP414 2.2 16.1 0.5
OP2 P:DC11 2.2 17.8 0.5
O11 A:PPV413 2.2 16.4 0.5
O A:HOH704 2.3 35.6 1.0
PA A:DCP414 2.6 15.7 0.5
P P:DC11 3.3 17.1 0.5
O2G A:DCP414 3.3 17.4 0.5
O3B A:DCP414 3.5 16.3 0.5
PB A:DCP414 3.5 15.9 0.5
O3G A:DCP414 3.6 16.4 0.5
P1 A:PPV413 3.7 15.6 0.5
O P:HOH206 3.7 30.0 1.0
PG A:DCP414 3.7 17.6 0.5
O5' A:DCP414 3.8 14.3 0.5
O2A A:DCP414 3.8 14.5 0.5
OP1 P:DC11 3.8 16.8 0.5
O32 A:PPV413 3.9 16.0 0.5
O5' P:DC11 3.9 16.2 0.5
OPP A:PPV413 4.2 15.6 0.5
O1B A:DCP414 4.2 15.8 0.5
O A:HOH699 4.3 18.7 1.0
O P:HOH201 4.3 34.7 1.0
P2 A:PPV413 4.5 16.4 0.5
O31 A:PPV413 4.5 15.4 0.5
O12 A:PPV413 4.5 15.3 0.5
O2B A:DCP414 4.6 15.3 0.5
O21 A:PPV413 4.6 14.7 0.5
O A:HOH705 4.6 37.7 1.0
O3' P:DC10 4.7 17.8 0.5
MG A:MG402 4.8 14.4 1.0
C5' A:DCP414 5.0 13.6 0.5

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 03:15:52 2024

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