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Sodium 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:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4rpz

Go back to Sodium Binding Sites List in 4rpz
Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na403

b:24.9
occ:1.00
 O A:VAL65 2.2 23.3 1.0
O D:HOH202 2.2 26.4 1.0
O A:HOH589 2.2 29.1 1.0
O A:LEU62 2.3 25.6 1.0
O A:LYS60 2.3 25.6 1.0
OP1 D:DC3 2.3 24.9 1.0
C A:VAL65 3.3 22.7 1.0
C A:LEU62 3.4 25.7 1.0
C A:LYS60 3.4 26.9 1.0
P D:DC3 3.6 24.4 1.0
N A:VAL65 3.7 21.8 1.0
CA A:VAL65 3.9 22.1 1.0
OP2 D:DC3 4.0 24.3 1.0
N A:LEU62 4.0 27.2 1.0
C A:LYS61 4.1 28.9 1.0
N A:GLY64 4.1 23.9 1.0
N A:PRO63 4.2 24.8 1.0
CA A:PRO63 4.2 24.8 1.0
CB A:VAL65 4.2 22.1 1.0
CD A:LYS60 4.2 31.9 1.0
CA A:LYS60 4.3 27.0 1.0
O A:LYS61 4.3 30.5 1.0
CA A:LEU62 4.3 26.5 1.0
N A:LYS61 4.4 28.8 1.0
CE A:LYS60 4.4 33.0 1.0
N A:GLY66 4.4 21.9 1.0
C A:PRO63 4.4 24.7 1.0
O3' D:DT2 4.5 22.7 1.0
CA A:LYS61 4.5 30.2 1.0
C A:GLY64 4.7 22.5 1.0
O5' D:DC3 4.7 24.2 1.0
CA A:GLY66 4.8 21.4 1.0
O A:ALA59 4.8 24.8 1.0
CG A:LYS60 4.9 30.8 1.0
CA A:GLY64 5.0 23.1 1.0

Sodium binding site 2 out of 4 in 4rpz

Go back to Sodium Binding Sites List in 4rpz
Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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:Na404

b:19.6
occ:1.00
 O A:THR101 2.2 18.5 1.0
OP1 P:DG9 2.2 21.3 1.0
O P:HOH208 2.2 23.6 1.0
O A:HOH517 2.2 18.5 1.0
O A:ILE106 2.3 18.9 1.0
O A:VAL103 2.3 19.5 1.0
C A:THR101 3.3 19.0 1.0
P P:DG9 3.3 23.8 1.0
C A:ILE106 3.3 18.8 1.0
C A:VAL103 3.3 19.0 1.0
OP2 P:DG9 3.5 22.3 1.0
N A:ILE106 3.6 19.0 1.0
N A:GLY105 3.9 18.6 1.0
CA A:THR101 4.0 18.9 1.0
CA A:SER104 4.0 19.1 1.0
CA A:ILE106 4.0 18.9 1.0
N A:SER104 4.0 19.1 1.0
N A:VAL103 4.1 18.8 1.0
C A:ARG102 4.2 19.8 1.0
O3' P:DC8 4.3 24.1 1.0
N A:ARG102 4.3 19.6 1.0
N A:GLY107 4.3 17.9 1.0
C A:SER104 4.3 18.6 1.0
CA A:VAL103 4.3 19.0 1.0
O5' P:DG9 4.5 22.8 1.0
CA A:ARG102 4.5 20.3 1.0
CB A:ILE106 4.5 19.5 1.0
C A:GLY105 4.5 19.0 1.0
CA A:GLY107 4.6 17.4 1.0
CB A:THR101 4.6 18.7 1.0
O A:ARG102 4.6 19.4 1.0
O A:LEU100 4.8 18.1 1.0
CA A:GLY105 4.8 18.7 1.0
C5' P:DG9 5.0 24.4 1.0

Sodium binding site 3 out of 4 in 4rpz

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Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na 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
A:Na405

b:35.8
occ:1.00
 O A:HOH593 2.2 33.6 1.0
OD1 A:ASP318 2.3 33.8 1.0
OD2 A:ASP321 2.3 33.8 1.0
CG A:ASP321 3.4 32.0 1.0
CG A:ASP318 3.5 31.6 1.0
O A:HOH608 3.5 35.0 1.0
N A:ASP318 3.8 28.6 1.0
CA A:ASP318 3.9 29.2 1.0
CG A:LYS317 4.0 33.7 1.0
CD A:LYS317 4.1 35.1 1.0
OD1 A:ASP321 4.1 31.4 1.0
NZ A:LYS317 4.1 36.4 1.0
C A:LYS317 4.2 29.5 1.0
CB A:LYS317 4.3 32.9 1.0
O A:HOH585 4.3 16.7 0.5
CB A:ASP318 4.3 30.3 1.0
OG A:SER315 4.4 30.1 1.0
CB A:ASP321 4.4 31.3 1.0
OD2 A:ASP318 4.4 32.5 1.0
O A:LYS317 4.5 29.2 1.0
CE A:LYS317 4.7 35.8 1.0
CA A:LYS317 4.9 30.9 1.0

Sodium binding site 4 out of 4 in 4rpz

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Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na binding site number 4 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
D:Na102

b:33.5
occ:1.00
 O1B D:DCP101 2.0 38.0 0.8
O2G D:DCP101 2.2 35.2 0.8
O D:HOH209 2.2 31.1 0.5
O D:HOH208 2.3 21.2 0.5
O D:HOH210 3.0 37.8 1.0
PB D:DCP101 3.2 34.9 0.8
PG D:DCP101 3.3 35.6 0.8
O3B D:DCP101 3.4 36.6 0.8
O1G D:DCP101 3.9 36.1 0.8
O2B D:DCP101 4.3 34.9 0.8
O3A D:DCP101 4.4 38.7 0.8
O3G D:DCP101 4.5 34.5 0.8

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: Mon Oct 7 18:17:50 2024

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