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Chlorine 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:

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

Chlorine binding site 1 out of 2 in 4rq7

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


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 Datp Soaked with MGCL2 For 1HR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:38.9
occ:1.00
 NH1 A:ARG299 2.7 47.0 1.0
OG1 A:THR297 3.2 27.1 1.0
ND2 A:ASN294 3.3 36.8 1.0
OD1 A:ASN294 3.8 33.1 1.0
CZ A:ARG299 3.9 45.2 1.0
CG2 A:THR297 3.9 27.6 1.0
CB A:TYR296 4.0 29.8 1.0
CG A:ASN294 4.0 37.5 1.0
CB A:THR297 4.2 27.8 1.0
CD2 A:TYR296 4.2 34.0 1.0
O A:HOH608 4.6 35.2 1.0
CG A:TYR296 4.6 32.5 1.0
N A:THR297 4.6 27.9 1.0
CD A:ARG299 4.6 38.5 1.0
NE A:ARG299 4.7 42.3 1.0
NH2 A:ARG299 4.7 47.2 1.0

Chlorine binding site 2 out of 2 in 4rq7

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


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 Datp Soaked with MGCL2 For 1HR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:36.0
occ:1.00
 O D:HOH206 2.7 32.0 1.0
O A:HOH546 3.0 48.6 1.0
N A:HIS34 3.1 20.2 1.0
C A:ALA32 3.3 20.5 1.0
CA A:ALA32 3.4 21.4 1.0
CB A:HIS34 3.4 22.3 1.0
CB A:ALA32 3.5 21.8 1.0
N A:ILE33 3.5 20.0 1.0
CD2 A:HIS34 3.6 23.5 1.0
CA A:HIS34 3.7 20.4 1.0
N A:LYS35 3.7 18.5 1.0
CG A:HIS34 3.8 22.7 1.0
O A:ALA32 3.8 20.1 1.0
C A:ILE33 4.1 19.9 1.0
C A:HIS34 4.2 19.7 1.0
O A:HOH510 4.2 32.7 1.0
CG A:LYS35 4.3 20.3 1.0
CA A:ILE33 4.4 21.2 1.0
O6 D:DG1 4.7 17.2 1.0
CB A:LYS35 4.7 19.4 1.0
CA A:LYS35 4.8 18.4 1.0
N A:ALA32 4.8 22.1 1.0
NE2 A:HIS34 4.8 24.0 1.0
CD A:LYS35 4.9 22.9 1.0
CG2 A:ILE33 4.9 23.3 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: Fri Jul 26 01:25:01 2024

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