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Chlorine in PDB 4rpy: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp Soaked with MGCL2 For 30 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 30 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 30 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 30 S, PDB code: 4rpy 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) 31.23 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.440, 79.530, 55.520, 90.00, 106.61, 90.00
R / Rfree (%) 19 / 23

Other elements in 4rpy:

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 30 S also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Sodium (Na) 7 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 30 S (pdb code 4rpy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 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 30 S, PDB code: 4rpy:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4rpy

Go back to Chlorine Binding Sites List in 4rpy
Chlorine 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 Dctp Soaked with MGCL2 For 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:31.9
occ:1.00
 O A:HOH621 2.9 30.1 1.0
N A:HIS135 3.1 13.5 1.0
O T:HOH242 3.1 38.4 1.0
CB A:HIS135 3.6 13.6 1.0
N A:HIS134 3.6 14.8 1.0
CB A:HIS134 3.7 15.6 1.0
OD1 A:ASN133 3.8 15.4 1.0
CG A:ASN133 3.8 15.1 1.0
CA A:HIS135 3.9 13.4 1.0
CA A:HIS134 3.9 14.7 1.0
CB A:ASN133 3.9 14.9 1.0
C A:HIS134 4.0 14.2 1.0
ND2 A:ASN133 4.3 15.2 1.0
C A:ASN133 4.3 14.6 1.0
CA A:ASN133 4.7 15.0 1.0
CG A:HIS134 4.7 16.4 1.0
O A:LEU228 4.8 16.1 1.0
ND1 A:HIS134 4.8 17.3 1.0
OP1 T:DT12 4.9 29.2 1.0
CG A:HIS135 4.9 13.8 1.0

Chlorine binding site 2 out of 4 in 4rpy

Go back to Chlorine Binding Sites List in 4rpy
Chlorine 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 Dctp Soaked with MGCL2 For 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:23.5
occ:1.00
 O A:HOH594 2.9 31.2 1.0
O A:HOH538 3.1 17.0 1.0
N A:CYS267 3.3 15.3 1.0
N A:TYR266 3.3 16.8 1.0
C A:GLN264 3.5 17.1 1.0
CA A:GLN264 3.5 17.0 1.0
CB A:TYR266 3.6 18.0 1.0
O A:GLN264 3.7 17.1 1.0
CA A:TYR266 3.8 16.9 1.0
O A:ASP263 3.9 17.2 1.0
SG A:CYS267 3.9 18.1 1.0
N A:TYR265 3.9 16.5 1.0
CB A:VAL313 4.0 22.5 1.0
C A:TYR266 4.0 16.2 1.0
CG1 A:VAL313 4.0 22.3 1.0
CB A:CYS267 4.1 16.0 1.0
CD2 A:TYR266 4.2 20.4 1.0
CA A:CYS267 4.3 15.9 1.0
C A:TYR265 4.3 16.9 1.0
CG A:TYR266 4.4 19.1 1.0
CB A:GLN264 4.5 17.1 1.0
N A:GLN264 4.5 17.1 1.0
O A:TYR296 4.5 15.7 1.0
C A:ASP263 4.6 17.6 1.0
O A:VAL313 4.6 20.9 1.0
CA A:TYR265 4.7 17.1 1.0
CG2 A:VAL313 4.8 22.6 1.0

Chlorine binding site 3 out of 4 in 4rpy

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Chlorine 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 Dctp Soaked with MGCL2 For 30 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 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:28.9
occ:1.00
 NH2 A:ARG299 2.9 29.2 1.0
O A:HOH625 3.2 24.3 1.0
OG1 A:THR297 3.2 19.7 1.0
NE A:ARG299 3.4 28.9 1.0
ND2 A:ASN294 3.5 16.3 1.0
CZ A:ARG299 3.6 30.1 1.0
O T:HOH208 3.6 37.6 1.0
O A:HOH655 3.8 44.1 1.0
CG2 A:THR297 3.9 18.3 1.0
CB A:TYR296 4.0 16.9 1.0
OD1 A:ASN294 4.1 16.4 1.0
CB A:THR297 4.2 18.4 1.0
CG A:ASN294 4.2 15.9 1.0
CD2 A:TYR296 4.3 17.7 1.0
CG A:TYR296 4.5 17.4 1.0
N A:THR297 4.7 17.0 1.0
CD A:ARG299 4.8 27.8 1.0
O A:HOH555 4.9 41.5 1.0
NH1 A:ARG299 4.9 31.8 1.0
O A:HOH598 5.0 22.5 1.0

Chlorine binding site 4 out of 4 in 4rpy

Go back to Chlorine Binding Sites List in 4rpy
Chlorine 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 Dctp Soaked with MGCL2 For 30 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Dctp Soaked with MGCL2 For 30 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:24.2
occ:1.00
 N A:HIS34 3.3 15.7 1.0
CA A:ALA32 3.4 16.4 1.0
C A:ALA32 3.4 16.1 1.0
CB A:ALA32 3.5 16.2 1.0
CB A:HIS34 3.5 17.3 1.0
N A:LYS35 3.6 14.1 1.0
N A:ILE33 3.7 15.4 1.0
CA A:HIS34 3.8 15.9 1.0
O A:ALA32 3.9 16.4 1.0
CD2 A:HIS34 3.9 18.5 1.0
CG A:HIS34 4.0 18.2 1.0
C A:HIS34 4.1 15.0 1.0
CG A:LYS35 4.3 14.1 1.0
C A:ILE33 4.3 15.9 1.0
O A:HOH636 4.4 23.2 1.0
CA A:ILE33 4.6 16.0 1.0
CB A:LYS35 4.6 14.0 1.0
CA A:LYS35 4.7 13.9 1.0
O6 D:DG1 4.8 16.0 1.0
N A:ALA32 4.9 16.4 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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