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Chlorine in PDB 4rq8: Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 MNCL2 For 35 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 MNCL2 For 35 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 MNCL2 For 35 S, PDB code: 4rq8 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) 40.79 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.220, 82.540, 54.740, 90.00, 110.89, 90.00
R / Rfree (%) 20.7 / 27

Other elements in 4rq8:

The structure of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Sodium (Na) 9 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 MNCL2 For 35 S (pdb code 4rq8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 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 MNCL2 For 35 S, PDB code: 4rq8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4rq8

Go back to Chlorine Binding Sites List in 4rq8
Chlorine binding site 1 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:29.3
occ:1.00
 NH2 A:ARG299 3.1 20.4 0.5
O T:HOH222 3.1 33.3 1.0
OG1 A:THR297 3.3 17.9 1.0
O T:HOH212 3.4 39.0 1.0
ND2 A:ASN294 3.4 15.7 1.0
O A:HOH623 3.4 22.7 1.0
NE A:ARG299 3.4 21.6 0.5
CZ A:ARG299 3.7 21.8 0.5
CG2 A:THR297 3.8 18.4 1.0
OD1 A:ASN294 4.0 15.0 1.0
NE A:ARG299 4.0 23.0 0.5
CB A:TYR296 4.1 17.9 1.0
CZ A:ARG299 4.1 24.1 0.5
CG A:ASN294 4.1 15.0 1.0
CB A:THR297 4.1 18.2 1.0
CD2 A:TYR296 4.3 19.8 1.0
NH2 A:ARG299 4.3 24.5 0.5
CD A:ARG299 4.5 22.5 0.5
CD A:ARG299 4.6 21.3 0.5
CG A:TYR296 4.6 18.6 1.0
NH1 A:ARG299 4.7 25.0 0.5
O T:HOH213 4.7 31.2 1.0
O A:HOH606 4.7 32.1 1.0
N A:THR297 4.8 17.3 1.0
O A:HOH510 4.8 18.2 1.0
NH1 A:ARG299 4.9 21.9 0.5

Chlorine binding site 2 out of 6 in 4rq8

Go back to Chlorine Binding Sites List in 4rq8
Chlorine binding site 2 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:24.2
occ:1.00
 N A:HIS34 3.3 17.5 1.0
C A:ALA32 3.3 17.6 1.0
CB A:HIS34 3.3 19.8 1.0
CA A:ALA32 3.4 17.2 1.0
N A:LYS35 3.5 18.3 1.0
CB A:ALA32 3.5 17.0 1.0
CD2 A:HIS34 3.6 20.7 1.0
N A:ILE33 3.6 17.8 1.0
O A:ALA32 3.7 17.8 1.0
CA A:HIS34 3.7 18.4 1.0
CG A:HIS34 3.8 20.3 1.0
CG A:LYS35 4.0 19.2 1.0
C A:HIS34 4.1 18.0 1.0
C A:ILE33 4.3 17.8 1.0
CB A:LYS35 4.5 18.9 1.0
CA A:ILE33 4.6 18.8 1.0
CA A:LYS35 4.6 18.2 1.0
N A:ALA32 4.8 17.8 1.0
NE2 A:HIS34 4.9 22.4 1.0
CD A:LYS35 4.9 19.6 1.0

Chlorine binding site 3 out of 6 in 4rq8

Go back to Chlorine Binding Sites List in 4rq8
Chlorine binding site 3 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl416

b:34.2
occ:1.00
 O A:HOH513 3.0 30.3 1.0
NH2 A:ARG183 3.1 22.9 1.0
N A:GLU335 3.2 28.9 1.0
CB A:SER334 3.6 29.4 1.0
CA A:SER334 3.7 29.8 1.0
C A:SER334 4.0 29.4 1.0
CB A:GLU335 4.0 31.1 1.0
CZ A:ARG183 4.0 22.6 1.0
OG A:SER334 4.1 30.0 1.0
NE A:ARG183 4.1 23.3 1.0
CA A:GLU335 4.2 29.0 1.0
CB A:SER275 4.2 18.8 1.0
CG A:GLU335 4.3 32.9 1.0
O A:GLU335 4.6 28.5 1.0
C A:GLU335 4.8 27.2 1.0
OG A:SER275 4.9 16.7 1.0
N A:SER334 5.0 30.1 1.0

Chlorine binding site 4 out of 6 in 4rq8

Go back to Chlorine Binding Sites List in 4rq8
Chlorine binding site 4 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 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 Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl417

b:61.0
occ:1.00
 ND2 A:ASN281 3.5 30.0 1.0
CB A:ASN281 3.7 26.4 1.0
CD1 A:PHE278 4.0 26.0 1.0
CA A:PHE278 4.2 20.7 1.0
CG A:ASN281 4.2 29.8 1.0
CH2 A:TRP325 4.4 31.7 1.0
NZ A:LYS48 4.6 32.1 1.0
O A:PHE278 4.6 20.6 1.0
CB A:PHE278 4.7 22.1 1.0
CE1 A:PHE278 4.7 26.5 1.0
CG A:PHE278 4.7 24.6 1.0
O A:HOH515 4.8 35.3 1.0
N A:PHE278 4.9 20.9 1.0
C A:PHE278 4.9 19.6 1.0
O A:ILE277 4.9 19.7 1.0

Chlorine binding site 5 out of 6 in 4rq8

Go back to Chlorine Binding Sites List in 4rq8
Chlorine binding site 5 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl418

b:36.9
occ:1.00
 O A:HOH532 2.8 38.2 1.0
ND1 A:HIS34 3.0 20.8 1.0
OXT A:ACT420 3.1 34.9 1.0
ND2 A:ASN37 3.2 23.8 1.0
N1 T:DC5 3.5 22.9 1.0
C2 T:DC5 3.6 22.5 1.0
CE1 A:HIS34 3.8 21.4 1.0
C6 T:DC5 3.9 22.1 1.0
C1' T:DC5 3.9 25.9 1.0
O2 T:DC5 3.9 21.4 1.0
CA A:HIS34 3.9 18.4 1.0
C2' T:DC5 3.9 25.3 1.0
CB A:ASN37 4.0 19.7 1.0
CG A:HIS34 4.0 20.3 1.0
N3 T:DC5 4.0 21.1 1.0
CG A:ASN37 4.1 21.6 1.0
N2 T:8OG6 4.1 22.7 1.0
CB A:HIS34 4.2 19.8 1.0
C5 T:DC5 4.3 22.1 1.0
C A:ACT420 4.3 37.8 1.0
C4 T:DC5 4.3 20.8 1.0
O T:HOH233 4.5 32.5 1.0
O A:HIS34 4.6 18.9 1.0
N A:HIS34 4.8 17.5 1.0
CH3 A:ACT420 4.8 38.6 1.0
C A:HIS34 4.8 18.0 1.0
O A:ILE33 4.8 15.1 1.0
NE2 A:HIS34 5.0 22.4 1.0

Chlorine binding site 6 out of 6 in 4rq8

Go back to Chlorine Binding Sites List in 4rq8
Chlorine binding site 6 out of 6 in the Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human Dna Polymerase Beta with Gapped Dna Containing An 8-Oxo-7,8- Dihydro-Guanine(8-Oxog) and Datp Soaked with MNCL2 For 35 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl419

b:49.6
occ:1.00
 N A:LEU82 3.2 28.1 1.0
NH1 A:ARG89 3.2 50.7 1.0
CA A:LYS81 3.8 30.0 1.0
O A:LEU82 3.8 26.2 1.0
CB A:LEU85 3.8 26.7 1.0
CB A:LYS81 3.8 31.9 1.0
C A:LYS81 4.0 28.7 1.0
CA A:LEU82 4.1 28.6 1.0
CZ A:ARG89 4.2 50.9 1.0
CB A:LEU82 4.2 28.5 1.0
CD1 A:LEU85 4.4 28.6 1.0
C A:LEU82 4.4 27.1 1.0
NH2 A:ARG89 4.5 50.5 1.0
N A:GLU86 4.6 33.0 1.0
CG A:LEU85 4.7 27.4 1.0
C A:LEU85 4.9 28.9 1.0
CA A:LEU85 4.9 27.1 1.0
CG A:GLU86 5.0 43.9 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 01:25:23 2024

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