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Sodium in PDB 4rq7: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 1HR

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 1HR

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 1HR:
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 1HR, PDB code: 4rq7 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) 45.40 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.330, 79.610, 55.830, 90.00, 109.56, 90.00
R / Rfree (%) 20.7 / 26.1

Other elements in 4rq7:

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 1HR also contains other interesting chemical elements:

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 Datp Soaked with MGCL2 For 1HR (pdb code 4rq7). 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 Datp Soaked with MGCL2 For 1HR, PDB code: 4rq7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4rq7

Go back to Sodium Binding Sites List in 4rq7
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 Datp Soaked with MGCL2 For 1HR


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 1HR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:19.9
occ:1.00
 OP1 P:DG9 2.3 17.2 0.6
OP1 P:DG9 2.3 17.2 0.5
O A:THR101 2.3 16.6 1.0
O A:ILE106 2.4 16.6 1.0
O P:HOH202 2.4 14.8 1.0
O P:HOH201 2.5 17.4 1.0
O A:VAL103 2.6 13.7 1.0
P P:DG9 3.3 17.7 0.6
C A:ILE106 3.3 16.4 1.0
C A:THR101 3.4 16.1 1.0
P P:DG9 3.4 17.7 0.5
C A:VAL103 3.5 14.2 1.0
OP2 P:DG9 3.5 17.6 0.6
OP2 P:DG9 3.7 17.7 0.5
N A:ILE106 3.8 15.1 1.0
CA A:THR101 3.9 16.0 1.0
O A:HOH537 4.1 28.6 1.0
CA A:ILE106 4.1 15.8 1.0
CA A:SER104 4.1 14.5 1.0
N A:SER104 4.2 14.6 1.0
N A:GLY105 4.2 15.5 1.0
N A:VAL103 4.3 14.0 1.0
N A:GLY107 4.3 16.4 1.0
CB A:THR101 4.3 16.2 1.0
O5' P:DG9 4.4 18.8 0.6
N A:ARG102 4.4 15.2 1.0
O3' P:DC8 4.4 17.6 1.0
C A:ARG102 4.5 15.0 1.0
CA A:GLY107 4.5 16.8 1.0
CA A:VAL103 4.5 13.7 1.0
C A:SER104 4.5 14.9 1.0
O5' P:DG9 4.5 18.3 0.5
CB A:ILE106 4.6 15.6 1.0
C A:GLY105 4.7 15.3 1.0
CA A:ARG102 4.8 15.7 1.0
OP2 P:DC10 4.8 25.3 0.5
C5' P:DG9 4.9 18.7 0.5
O A:ARG102 4.9 14.9 1.0
O A:LEU100 4.9 16.1 1.0

Sodium binding site 2 out of 4 in 4rq7

Go back to Sodium Binding Sites List in 4rq7
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 Datp Soaked with MGCL2 For 1HR


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 1HR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:29.7
occ:1.00
 O D:HOH202 2.3 28.6 1.0
O A:VAL65 2.3 25.7 1.0
O A:HOH549 2.4 29.1 1.0
O A:LEU62 2.5 26.8 1.0
O A:LYS60 2.5 29.8 1.0
OP1 D:DC3 2.7 25.5 1.0
C A:VAL65 3.4 23.6 1.0
C A:LEU62 3.5 27.6 1.0
C A:LYS60 3.6 29.6 1.0
P D:DC3 3.7 23.4 1.0
OP2 D:DC3 3.8 22.5 1.0
N A:VAL65 3.8 22.3 1.0
CA A:VAL65 4.1 22.6 1.0
N A:GLY64 4.1 23.3 1.0
CA A:PRO63 4.2 26.2 1.0
N A:LEU62 4.2 27.2 1.0
N A:PRO63 4.3 27.4 1.0
C A:LYS61 4.3 29.5 1.0
CA A:LYS60 4.3 29.4 1.0
CB A:VAL65 4.4 23.6 1.0
N A:GLY66 4.4 22.1 1.0
O A:HOH550 4.4 43.9 1.0
CG A:LYS60 4.5 35.4 1.0
CA A:LEU62 4.5 26.8 1.0
O A:LYS61 4.5 30.7 1.0
O3' D:DT2 4.6 22.3 1.0
C A:PRO63 4.6 25.6 1.0
N A:LYS61 4.6 29.4 1.0
CA A:GLY66 4.7 21.2 1.0
CA A:LYS61 4.8 31.0 1.0
C A:GLY64 4.8 22.4 1.0
CB A:LYS60 5.0 32.8 1.0
CA A:GLY64 5.0 23.0 1.0
O5' D:DC3 5.0 23.4 1.0

Sodium binding site 3 out of 4 in 4rq7

Go back to Sodium Binding Sites List in 4rq7
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 Datp Soaked with MGCL2 For 1HR


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 1HR within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:48.4
occ:1.00
 O T:HOH233 1.7 28.8 0.5
O D:HOH205 2.3 40.2 1.0
OXT T:ACT102 2.4 45.2 1.0
O T:HOH205 2.8 27.5 1.0
O D:HOH211 2.9 36.7 1.0
C T:ACT102 3.4 45.2 1.0
CH3 T:ACT102 3.9 42.9 1.0
O T:HOH214 4.3 52.0 1.0
O D:HOH213 4.3 44.8 1.0
O D:HOH204 4.4 32.6 1.0
O T:ACT102 4.4 39.1 1.0
O4' D:DG4 4.4 35.2 1.0
C4' D:DG4 4.4 36.5 1.0
C5' D:DG4 4.5 34.2 1.0
O2 D:DC3 4.9 24.4 1.0

Sodium binding site 4 out of 4 in 4rq7

Go back to Sodium Binding Sites List in 4rq7
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 Datp Soaked with MGCL2 For 1HR


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 Datp Soaked with MGCL2 For 1HR within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:48.3
occ:1.00
 O T:HOH223 2.0 35.2 1.0
O T:HOH227 2.1 45.3 1.0
O T:HOH224 2.1 29.9 1.0
O T:HOH222 2.1 40.7 1.0
O T:HOH231 2.2 31.3 0.5
O P:HOH216 3.8 44.9 1.0
O T:HOH225 3.9 56.6 1.0
N7 T:DA14 3.9 29.9 1.0
O6 T:DG15 4.1 27.0 1.0
N7 T:DG15 4.1 30.4 1.0
O T:HOH218 4.2 38.9 1.0
C8 T:DA14 4.4 30.7 1.0
N4 T:DC16 4.6 25.9 1.0
O6 P:DG1 4.8 21.1 1.0
C5 T:DA14 4.9 28.4 1.0
C6 T:DG15 4.9 27.2 1.0
C5 T:DG15 4.9 29.1 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 18:19:47 2024

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