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Sodium 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:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 5 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 30 S (pdb code 4rq4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 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 30 S, PDB code: 4rq4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4rq4

Go back to Sodium Binding Sites List in 4rq4
Sodium binding site 1 out of 2 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 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:20.2
occ:1.00
 O A:THR101 2.2 21.0 1.0
O P:HOH201 2.3 29.9 1.0
O A:VAL103 2.4 21.7 1.0
O P:HOH202 2.4 34.8 1.0
OP1 P:DG9 2.4 28.8 1.0
O A:ILE106 2.4 25.8 1.0
C A:VAL103 3.3 22.5 1.0
C A:THR101 3.3 22.3 1.0
P P:DG9 3.4 30.9 1.0
C A:ILE106 3.5 21.0 1.0
OP2 P:DG9 3.6 30.0 1.0
N A:ILE106 3.8 19.8 1.0
CA A:SER104 4.0 22.4 1.0
N A:SER104 4.0 22.6 1.0
N A:GLY105 4.0 21.6 1.0
CA A:THR101 4.1 22.2 1.0
N A:VAL103 4.1 24.0 1.0
C A:ARG102 4.2 26.1 1.0
CA A:ILE106 4.2 20.1 1.0
CA A:VAL103 4.3 23.1 1.0
N A:ARG102 4.3 24.5 1.0
C A:SER104 4.3 22.5 1.0
N A:GLY107 4.4 20.6 1.0
O5' P:DG9 4.5 27.3 1.0
CA A:ARG102 4.5 26.6 1.0
O A:ARG102 4.5 27.6 1.0
O3' P:DC8 4.6 30.1 1.0
CB A:ILE106 4.6 20.5 1.0
CA A:GLY107 4.7 20.2 1.0
CB A:THR101 4.7 22.0 1.0
C A:GLY105 4.7 20.7 1.0
O A:LEU100 4.8 21.3 1.0
CA A:GLY105 4.9 20.9 1.0

Sodium binding site 2 out of 2 in 4rq4

Go back to Sodium Binding Sites List in 4rq4
Sodium binding site 2 out of 2 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 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:31.0
occ:1.00
 O D:HOH101 2.3 43.9 1.0
O A:LEU62 2.5 35.4 1.0
O A:VAL65 2.5 30.6 1.0
O A:LYS60 2.6 35.5 1.0
OP1 D:DC3 2.6 37.8 1.0
OP2 D:DC3 3.5 37.4 1.0
P D:DC3 3.5 36.8 1.0
C A:VAL65 3.5 29.1 1.0
C A:LEU62 3.6 35.5 1.0
C A:LYS60 3.7 38.9 1.0
N A:VAL65 3.9 31.5 1.0
N A:GLY64 4.1 32.7 1.0
CA A:VAL65 4.2 29.8 1.0
CA A:PRO63 4.2 31.7 1.0
N A:LEU62 4.3 38.8 1.0
C A:LYS61 4.3 41.5 1.0
N A:PRO63 4.4 32.1 1.0
N A:GLY66 4.5 30.0 1.0
O3' D:DT2 4.5 37.0 1.0
CB A:VAL65 4.5 27.3 1.0
C A:PRO63 4.6 34.0 1.0
CA A:LYS60 4.6 38.9 1.0
CA A:LEU62 4.6 37.1 1.0
O A:LYS61 4.6 39.9 1.0
CA A:GLY66 4.7 28.9 1.0
CG A:LYS60 4.7 47.5 1.0
N A:LYS61 4.7 39.4 1.0
CA A:LYS61 4.7 42.3 1.0
O5' D:DC3 4.8 37.9 1.0
C A:GLY64 4.9 32.8 1.0
NZ A:LYS60 4.9 56.0 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 18:18:49 2024

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