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Sodium in PDB 4rq0: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MGCL2 For 80 S, PDB code: 4rq0 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) 44.18 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.610, 79.540, 55.460, 90.00, 106.68, 90.00
R / Rfree (%) 20.8 / 26.8

Other elements in 4rq0:

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 80 S also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 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 80 S (pdb code 4rq0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 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 80 S, PDB code: 4rq0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4rq0

Go back to Sodium Binding Sites List in 4rq0
Sodium 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 80 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 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:22.1
occ:1.00
 OD2 A:ASP256 2.2 17.6 1.0
OD1 A:ASP192 2.2 20.0 1.0
OD2 A:ASP190 2.2 22.8 1.0
OP1 P:DC11 2.2 22.8 1.0
O3' P:DC10 2.3 23.6 1.0
P P:DC11 2.8 23.6 1.0
CG A:ASP190 3.1 22.3 1.0
CG A:ASP192 3.2 19.6 1.0
OD1 A:ASP190 3.3 23.1 1.0
CG A:ASP256 3.4 18.2 1.0
OD2 A:ASP192 3.5 19.7 1.0
C3' P:DC10 3.5 22.9 1.0
MG A:MG403 3.7 23.0 1.0
C4' P:DC10 3.8 23.5 1.0
OP2 P:DC11 3.8 23.8 1.0
C5' P:DC10 3.9 23.7 1.0
CB A:ASP256 3.9 17.3 1.0
O5' P:DC11 4.0 22.0 1.0
C5' P:DC11 4.2 20.3 1.0
OD1 A:ASP256 4.4 18.7 1.0
CB A:ASP190 4.5 21.4 1.0
CB A:ASP192 4.6 19.7 1.0
C2' P:DC10 4.6 21.8 1.0
O5' P:DC10 4.8 24.1 1.0
O P:HOH202 4.8 30.4 1.0
O A:MET191 4.8 19.7 1.0
OP1 P:DC10 4.9 24.4 1.0
NH2 A:ARG254 4.9 15.6 1.0
O A:HOH576 4.9 32.8 1.0
O11 A:PPV401 5.0 27.4 1.0
N A:ASP256 5.0 16.3 1.0

Sodium binding site 2 out of 3 in 4rq0

Go back to Sodium Binding Sites List in 4rq0
Sodium 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 80 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 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:14.2
occ:1.00
 O A:THR101 2.2 17.5 1.0
OP1 P:DG9 2.2 26.0 1.0
O P:HOH201 2.3 16.7 1.0
O A:VAL103 2.4 15.0 1.0
O A:ILE106 2.6 14.8 1.0
C A:THR101 3.3 17.9 1.0
C A:VAL103 3.3 15.9 1.0
P P:DG9 3.4 25.0 1.0
C A:ILE106 3.5 14.3 1.0
OP2 P:DG9 3.7 24.6 1.0
N A:ILE106 3.8 13.1 1.0
CA A:SER104 4.0 15.0 1.0
N A:GLY105 4.0 14.5 1.0
N A:VAL103 4.0 16.6 1.0
N A:SER104 4.0 14.9 1.0
CA A:THR101 4.1 17.3 1.0
C A:ARG102 4.1 18.2 1.0
CA A:ILE106 4.2 13.1 1.0
N A:ARG102 4.3 18.5 1.0
CA A:VAL103 4.3 16.3 1.0
N A:GLY107 4.4 14.9 1.0
C A:SER104 4.4 14.7 1.0
CA A:ARG102 4.4 19.3 1.0
O3' P:DC8 4.4 23.9 1.0
O5' P:DG9 4.5 24.9 1.0
O A:ARG102 4.5 18.4 1.0
CB A:ILE106 4.6 12.5 1.0
CA A:GLY107 4.6 15.5 1.0
CB A:THR101 4.7 17.1 1.0
C A:GLY105 4.7 13.6 1.0
O A:LEU100 4.8 15.6 1.0
CA A:GLY105 4.9 14.1 1.0

Sodium binding site 3 out of 3 in 4rq0

Go back to Sodium Binding Sites List in 4rq0
Sodium 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 80 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 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:25.2
occ:1.00
 O A:VAL65 2.2 20.7 1.0
O A:LYS60 2.5 25.6 1.0
O A:HOH548 2.6 23.4 1.0
OP1 D:DC3 2.7 23.7 1.0
O A:LEU62 2.8 22.7 1.0
OP2 D:DC3 3.4 24.2 1.0
C A:VAL65 3.4 20.4 1.0
P D:DC3 3.5 23.9 1.0
C A:LYS60 3.6 28.6 1.0
C A:LEU62 4.0 23.9 1.0
N A:VAL65 4.1 20.9 1.0
CA A:VAL65 4.3 20.4 1.0
CA A:LYS60 4.3 28.8 1.0
N A:GLY66 4.4 20.1 1.0
N A:GLY64 4.4 20.8 1.0
CA A:GLY66 4.5 19.4 1.0
C A:LYS61 4.5 29.0 1.0
N A:LEU62 4.5 26.6 1.0
CG A:LYS60 4.5 33.7 1.0
O3' D:DT2 4.6 22.6 1.0
CB A:VAL65 4.6 20.1 1.0
N A:LYS61 4.6 29.9 1.0
O A:LYS61 4.7 30.3 1.0
CA A:PRO63 4.7 22.3 1.0
O5' D:DC3 4.7 24.8 1.0
N A:PRO63 4.8 22.5 1.0
CA A:LYS61 4.8 29.8 1.0
CA A:LEU62 4.9 24.7 1.0
C A:PRO63 5.0 22.0 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: Mon Oct 7 18:17:50 2024

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