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Chlorine 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
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4rq0

Go back to Chlorine Binding Sites List in 4rq0
Chlorine 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 Dctp Soaked with MGCL2 For 80 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl407

b:36.2
occ:1.00
 O A:HOH558 3.1 33.7 1.0
N A:CYS267 3.2 21.3 1.0
N A:TYR266 3.2 21.7 1.0
C A:GLN264 3.3 21.6 1.0
CA A:GLN264 3.4 21.4 1.0
O A:GLN264 3.4 21.0 1.0
CB A:TYR266 3.7 22.3 1.0
CA A:TYR266 3.7 22.0 1.0
N A:TYR265 3.8 20.9 1.0
SG A:CYS267 3.9 24.9 1.0
C A:TYR266 3.9 21.2 1.0
CG1 A:VAL313 4.0 27.4 1.0
O A:ASP263 4.0 20.7 1.0
CB A:CYS267 4.0 22.5 1.0
CB A:VAL313 4.1 27.4 1.0
CD2 A:TYR266 4.1 24.0 1.0
C A:TYR265 4.2 21.3 1.0
CA A:CYS267 4.2 21.9 1.0
CG A:TYR266 4.4 23.1 1.0
N A:GLN264 4.4 22.0 1.0
CB A:GLN264 4.4 21.2 1.0
CA A:TYR265 4.5 21.2 1.0
C A:ASP263 4.6 21.4 1.0
O A:VAL313 4.6 27.1 1.0
O A:TYR296 4.6 22.3 1.0
CG2 A:VAL313 4.9 28.2 1.0

Chlorine binding site 2 out of 2 in 4rq0

Go back to Chlorine Binding Sites List in 4rq0
Chlorine 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 Dctp Soaked with MGCL2 For 80 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl408

b:27.0
occ:1.00
 N A:HIS34 3.3 23.0 1.0
C A:ALA32 3.5 20.9 1.0
CA A:ALA32 3.5 20.6 1.0
N A:LYS35 3.6 20.0 1.0
CB A:ALA32 3.6 20.1 1.0
CB A:HIS34 3.6 24.2 1.0
N A:ILE33 3.7 20.5 1.0
CA A:HIS34 3.9 22.9 1.0
O A:ALA32 3.9 21.8 1.0
CD2 A:HIS34 4.0 26.4 1.0
CG A:HIS34 4.1 26.0 1.0
CG A:LYS35 4.1 17.6 1.0
C A:HIS34 4.2 21.6 1.0
C A:ILE33 4.4 22.0 1.0
CB A:LYS35 4.6 18.3 1.0
CA A:ILE33 4.6 20.9 1.0
O A:HOH565 4.6 23.1 1.0
CA A:LYS35 4.7 19.2 1.0
O6 D:DG1 4.7 20.8 1.0
N A:ALA32 5.0 20.9 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: Sat Dec 12 11:11:54 2020

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