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Chlorine in PDB 4rpz: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp 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 Dctp 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 Dctp 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 Dctp Soaked with MGCL2 For 60 S, PDB code: 4rpz 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) 44.19 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.410, 79.320, 55.410, 90.00, 106.20, 90.00
R / Rfree (%) 19.5 / 25.1

Other elements in 4rpz:

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 60 S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
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 Dctp Soaked with MGCL2 For 60 S (pdb code 4rpz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 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 60 S, PDB code: 4rpz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4rpz

Go back to Chlorine Binding Sites List in 4rpz
Chlorine binding site 1 out of 3 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 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 Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:31.3
occ:1.00
 N A:CYS267 3.0 22.0 1.0
O A:HOH561 3.1 17.3 1.0
N A:TYR266 3.4 22.9 1.0
O A:HOH582 3.4 32.3 1.0
C A:GLN264 3.5 23.3 1.0
CA A:GLN264 3.5 23.6 1.0
CB A:TYR266 3.6 23.6 1.0
O A:GLN264 3.7 22.8 1.0
CA A:TYR266 3.7 23.2 1.0
SG A:CYS267 3.8 23.7 1.0
CB A:CYS267 3.8 22.7 1.0
C A:TYR266 3.8 22.4 1.0
CA A:CYS267 4.0 22.2 1.0
N A:TYR265 4.0 23.5 1.0
O A:ASP263 4.0 24.8 1.0
CG1 A:VAL313 4.0 26.9 1.0
CB A:VAL313 4.1 27.0 1.0
C A:TYR265 4.3 22.7 1.0
CD2 A:TYR266 4.4 25.3 1.0
O A:TYR296 4.4 22.9 1.0
CG A:TYR266 4.4 24.5 1.0
CB A:GLN264 4.5 23.3 1.0
N A:GLN264 4.5 24.3 1.0
C A:ASP263 4.7 24.5 1.0
CA A:TYR265 4.7 23.2 1.0
CG2 A:VAL313 4.7 26.7 1.0
O A:VAL313 4.8 25.7 1.0
O A:TYR266 4.9 21.5 1.0

Chlorine binding site 2 out of 3 in 4rpz

Go back to Chlorine Binding Sites List in 4rpz
Chlorine binding site 2 out of 3 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 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 Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:31.7
occ:1.00
 OG1 A:THR297 2.9 24.8 1.0
O A:HOH563 3.1 31.3 1.0
NH2 A:ARG299 3.1 36.0 1.0
ND2 A:ASN294 3.4 24.5 1.0
NE A:ARG299 3.4 35.5 1.0
CZ A:ARG299 3.7 36.5 1.0
OD1 A:ASN294 3.9 23.9 1.0
CG2 A:THR297 3.9 23.7 1.0
CB A:TYR296 3.9 23.9 1.0
CB A:THR297 4.0 23.9 1.0
CG A:ASN294 4.1 24.5 1.0
CD2 A:TYR296 4.2 23.9 1.0
CG A:TYR296 4.5 24.0 1.0
N A:THR297 4.6 23.5 1.0
CD A:ARG299 4.7 34.1 1.0
O A:HOH584 4.8 27.1 1.0
CA A:THR297 4.9 24.3 1.0

Chlorine binding site 3 out of 3 in 4rpz

Go back to Chlorine Binding Sites List in 4rpz
Chlorine binding site 3 out of 3 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 60 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine (8-Oxog)and Dctp Soaked with MGCL2 For 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:25.8
occ:1.00
 N A:HIS34 3.3 20.5 1.0
C A:ALA32 3.4 21.1 1.0
CA A:ALA32 3.4 21.5 1.0
CB A:ALA32 3.4 20.7 1.0
CB A:HIS34 3.5 22.4 1.0
N A:LYS35 3.5 19.3 1.0
O A:ALA32 3.7 22.6 1.0
N A:ILE33 3.7 20.2 1.0
CA A:HIS34 3.8 21.0 1.0
CD2 A:HIS34 4.0 24.4 1.0
CG A:LYS35 4.0 21.3 1.0
CG A:HIS34 4.1 23.9 1.0
C A:HIS34 4.1 19.7 1.0
C A:ILE33 4.3 20.9 1.0
CB A:LYS35 4.4 20.2 1.0
O A:HOH508 4.6 26.6 1.0
CA A:LYS35 4.6 19.3 1.0
CA A:ILE33 4.6 20.6 1.0
O6 D:DG1 4.7 18.7 1.0
N A:ALA32 4.8 22.3 1.0
CD A:LYS35 4.9 22.9 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: Fri Jul 26 01:22:54 2024

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