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Sodium 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:

Magnesium (Mg) 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 Datp Soaked with MGCL2 For 80 S (pdb code 4rq6). 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 Datp Soaked with MGCL2 For 80 S, PDB code: 4rq6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4rq6

Go back to Sodium Binding Sites List in 4rq6
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 Datp 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 Datp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:28.6
occ:1.00
 OD1 A:ASP192 2.2 29.3 1.0
OD2 A:ASP190 2.2 36.8 1.0
OD2 A:ASP256 2.3 28.9 1.0
OP1 P:DA11 2.3 28.7 1.0
O3' P:DC10 2.5 32.3 1.0
P P:DA11 2.9 31.3 1.0
CG A:ASP190 3.0 33.2 1.0
OD1 A:ASP190 3.0 32.9 1.0
CG A:ASP192 3.1 27.7 1.0
OD2 A:ASP192 3.3 28.6 1.0
CG A:ASP256 3.4 26.4 1.0
MG A:MG402 3.5 28.9 1.0
C3' P:DC10 3.7 32.7 1.0
C4' P:DC10 3.9 32.3 1.0
OP2 P:DA11 4.0 28.6 1.0
CB A:ASP256 4.0 25.8 1.0
O5' P:DA11 4.1 28.7 1.0
C5' P:DC10 4.1 32.3 1.0
C5' P:DA11 4.3 28.2 1.0
OD1 A:ASP256 4.4 26.4 1.0
CB A:ASP190 4.4 31.2 1.0
CB A:ASP192 4.5 28.5 1.0
O P:HOH205 4.6 39.1 1.0
C2' P:DC10 4.7 32.6 1.0
O A:MET191 4.7 26.0 1.0
NH2 A:ARG254 4.8 28.6 1.0
C A:MET191 4.9 27.0 1.0
CA A:ASP192 4.9 27.6 1.0
OP1 P:DC10 4.9 31.9 1.0
O5' P:DC10 4.9 31.2 1.0
N A:ASP256 5.0 23.9 1.0

Sodium binding site 2 out of 3 in 4rq6

Go back to Sodium Binding Sites List in 4rq6
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 Datp 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 Datp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:58.2
occ:1.00
 O A:LYS60 2.4 51.5 1.0
OP1 D:DC3 2.5 53.2 1.0
O A:LEU62 2.6 46.0 1.0
O A:VAL65 2.7 50.9 1.0
C A:LYS60 3.5 53.6 1.0
C A:VAL65 3.6 46.2 1.0
C A:LEU62 3.6 48.0 1.0
P D:DC3 3.6 56.7 1.0
OP2 D:DC3 3.9 56.8 1.0
N A:VAL65 4.0 42.5 1.0
O A:LYS61 4.1 56.3 1.0
C A:LYS61 4.1 53.4 1.0
CA A:PRO63 4.2 48.2 1.0
CA A:VAL65 4.2 44.2 1.0
CA A:LYS60 4.3 51.0 1.0
N A:PRO63 4.3 49.0 1.0
N A:GLY64 4.3 45.0 1.0
N A:LEU62 4.4 52.7 1.0
N A:LYS61 4.5 55.2 1.0
N A:GLY66 4.5 47.2 1.0
CG A:LYS60 4.5 55.1 1.0
CB A:VAL65 4.6 44.8 1.0
C A:PRO63 4.6 46.4 1.0
CA A:LYS61 4.6 55.5 1.0
CA A:LEU62 4.6 48.6 1.0
O3' D:DT2 4.7 57.0 1.0
O5' D:DC3 4.8 56.9 1.0
CA A:GLY66 4.8 46.7 1.0
O A:ALA59 4.9 41.0 1.0
C A:GLY64 4.9 45.1 1.0

Sodium binding site 3 out of 3 in 4rq6

Go back to Sodium Binding Sites List in 4rq6
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 Datp 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 Datp Soaked with MGCL2 For 80 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:31.5
occ:1.00
 O A:THR101 2.3 29.5 1.0
O A:HOH529 2.3 33.7 1.0
OP1 P:DG9 2.3 31.9 1.0
O A:ILE106 2.4 27.6 1.0
O A:VAL103 2.6 27.8 1.0
O P:HOH201 2.6 31.3 1.0
P P:DG9 3.3 30.4 1.0
C A:THR101 3.4 28.1 1.0
OP2 P:DG9 3.4 31.7 1.0
C A:ILE106 3.5 27.7 1.0
C A:VAL103 3.6 26.2 1.0
CA A:SER104 4.0 25.8 1.0
CA A:THR101 4.1 29.1 1.0
N A:GLY105 4.1 28.3 1.0
N A:ILE106 4.1 28.2 1.0
N A:SER104 4.2 24.5 1.0
N A:VAL103 4.2 27.6 1.0
CA A:ILE106 4.3 27.4 1.0
O3' P:DC8 4.3 30.8 1.0
N A:GLY107 4.4 28.4 1.0
C A:ARG102 4.4 28.6 1.0
N A:ARG102 4.4 27.5 1.0
C A:SER104 4.5 27.5 1.0
O5' P:DG9 4.5 29.4 1.0
CA A:VAL103 4.6 26.6 1.0
CA A:GLY107 4.6 28.8 1.0
CB A:THR101 4.6 28.7 1.0
CA A:ARG102 4.7 29.1 1.0
CB A:ILE106 4.7 29.1 1.0
C A:GLY105 4.8 28.8 1.0
O A:ARG102 4.9 28.6 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 18:19:44 2024

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