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Chlorine in PDB 4rq5: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Datp Soaked with MGCL2 For 60 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 60 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 60 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 60 S, PDB code: 4rq5 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) 50.00 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.212, 79.702, 55.384, 90.00, 106.66, 90.00
R / Rfree (%) 19.6 / 26.6

Other elements in 4rq5:

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 60 S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Sodium (Na) 2 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 60 S (pdb code 4rq5). 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 60 S, PDB code: 4rq5:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4rq5

Go back to Chlorine Binding Sites List in 4rq5
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 60 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 Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:40.8
occ:1.00
 ND2 A:ASN294 3.0 31.0 1.0
OG1 A:THR297 3.1 33.6 1.0
O A:HOH501 3.2 38.8 1.0
NH1 A:ARG299 3.7 61.1 1.0
CZ A:ARG299 3.8 57.9 1.0
CB A:TYR296 3.8 31.4 1.0
CG2 A:THR297 3.9 29.8 1.0
CG A:ASN294 4.0 31.2 1.0
OD1 A:ASN294 4.1 30.2 1.0
NH2 A:ARG299 4.1 57.8 1.0
CB A:THR297 4.1 30.6 1.0
CD2 A:TYR296 4.2 30.7 1.0
NE A:ARG299 4.3 47.5 1.0
CG A:TYR296 4.4 30.7 1.0
O A:HOH555 4.6 43.2 1.0
N A:THR297 4.7 31.0 1.0
CD A:ARG299 4.8 42.9 1.0
CA A:TYR296 5.0 31.4 1.0

Chlorine binding site 2 out of 2 in 4rq5

Go back to Chlorine Binding Sites List in 4rq5
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 60 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 Datp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:44.8
occ:1.00
 N A:CYS267 3.2 32.6 1.0
N A:TYR266 3.3 32.9 1.0
C A:GLN264 3.4 31.4 1.0
CA A:GLN264 3.4 32.7 1.0
O A:GLN264 3.5 32.6 1.0
CB A:TYR266 3.6 34.8 1.0
CA A:TYR266 3.8 34.2 1.0
SG A:CYS267 3.8 35.5 1.0
N A:TYR265 3.8 32.0 1.0
CB A:CYS267 3.9 32.4 1.0
C A:TYR266 3.9 34.0 1.0
CB A:VAL313 4.1 39.6 1.0
O A:ASP263 4.1 34.5 1.0
CA A:CYS267 4.2 32.9 1.0
CG1 A:VAL313 4.2 40.0 1.0
CD2 A:TYR266 4.3 40.1 1.0
C A:TYR265 4.3 32.9 1.0
CB A:GLN264 4.4 33.4 1.0
CG A:TYR266 4.4 37.7 1.0
N A:GLN264 4.5 33.0 1.0
O A:VAL313 4.7 42.4 1.0
C A:ASP263 4.7 32.4 1.0
CA A:TYR265 4.7 33.0 1.0
O A:TYR296 4.7 29.6 1.0
CG2 A:VAL313 4.7 38.1 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: Fri Jul 26 01:24:54 2024

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