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Chlorine in PDB 3rh5: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)

Enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)

All present enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp), PDB code: 3rh5 was solved by N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.70 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.220, 79.920, 55.090, 90.00, 107.93, 90.00
R / Rfree (%) 20.8 / 28.1

Other elements in 3rh5:

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) also contains other interesting chemical elements:

Manganese (Mn) 7 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) (pdb code 3rh5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp), PDB code: 3rh5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3rh5

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Chlorine binding site 1 out of 5 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl351

b:42.1
occ:1.00
 OG1 A:THR297 3.2 34.9 1.0
ND2 A:ASN294 3.4 29.1 1.0
O A:HOH536 3.4 42.5 1.0
NE A:ARG299 3.9 37.5 1.0
OD1 A:ASN294 4.0 31.8 1.0
CB A:TYR296 4.1 33.5 1.0
CZ A:ARG299 4.1 40.7 1.0
CG A:ASN294 4.1 26.8 1.0
CG2 A:THR297 4.2 32.1 1.0
CB A:THR297 4.3 35.1 1.0
NH2 A:ARG299 4.3 40.9 1.0
CD A:ARG299 4.4 37.0 1.0
CD2 A:TYR296 4.5 30.5 1.0
NH1 A:ARG299 4.7 45.7 1.0
CG A:TYR296 4.7 28.6 1.0
N A:THR297 4.8 29.0 1.0

Chlorine binding site 2 out of 5 in 3rh5

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Chlorine binding site 2 out of 5 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl352

b:42.2
occ:1.00
 NH1 A:ARG89 3.1 39.2 1.0
N A:LEU82 3.3 29.3 1.0
O A:HOH490 3.5 36.5 1.0
OE2 A:GLU86 3.5 43.0 1.0
CA A:LYS81 3.7 34.3 1.0
C A:LYS81 4.0 33.6 1.0
CZ A:ARG89 4.0 42.1 1.0
NH2 A:ARG89 4.0 43.5 1.0
CB A:LYS81 4.1 35.3 1.0
CB A:LEU85 4.1 32.1 1.0
O A:LEU82 4.1 35.5 1.0
CD1 A:LEU85 4.3 30.3 1.0
CA A:LEU82 4.3 36.1 1.0
CD A:GLU86 4.4 43.8 1.0
CG A:GLU86 4.4 37.2 1.0
CB A:LEU82 4.4 33.7 1.0
C A:LEU82 4.6 35.9 1.0
O A:GLY80 4.7 34.0 1.0
CG A:LYS81 4.8 36.1 1.0
CG A:LEU85 4.8 31.5 1.0
N A:GLU86 4.9 40.2 1.0
O A:HOH381 4.9 29.8 1.0
N A:LYS81 5.0 33.4 1.0

Chlorine binding site 3 out of 5 in 3rh5

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Chlorine binding site 3 out of 5 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl353

b:42.7
occ:1.00
 NE2 A:GLN159 2.7 29.4 1.0
O A:HOH422 3.0 30.9 1.0
N A:VAL177 3.0 28.9 1.0
CB A:VAL177 3.8 24.9 1.0
CA A:THR176 3.8 26.2 1.0
C A:THR176 3.9 27.0 1.0
CA A:VAL177 3.9 23.6 1.0
CD A:GLN159 4.0 27.5 1.0
O A:HOH556 4.0 41.6 1.0
CG2 A:VAL177 4.1 23.9 1.0
O A:VAL177 4.1 27.1 1.0
O A:ALA175 4.2 25.9 1.0
CG2 A:THR176 4.3 25.8 1.0
C A:VAL177 4.5 27.9 1.0
CG A:GLN159 4.6 25.6 1.0
CD2 A:LEU163 4.6 31.1 1.0
O A:HOH488 4.7 36.2 1.0
CB A:THR176 4.7 31.2 1.0
CE2 A:PHE181 4.9 27.0 1.0
N A:THR176 4.9 24.7 1.0
OE1 A:GLN159 4.9 26.6 1.0
O A:HOH445 4.9 30.4 1.0
C A:ALA175 5.0 28.6 1.0

Chlorine binding site 4 out of 5 in 3rh5

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Chlorine binding site 4 out of 5 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl354

b:48.8
occ:1.00
 N A:LYS331 3.2 31.1 1.0
CD A:PRO330 3.4 32.3 1.0
CB A:PRO330 3.5 29.1 1.0
CG A:LYS331 3.6 35.2 1.0
N A:PRO330 3.6 34.4 1.0
CB A:LYS331 3.7 37.3 1.0
CG A:PRO330 3.7 28.2 1.0
CB A:GLU329 3.8 35.5 1.0
OE1 A:GLU329 3.9 44.7 1.0
CA A:PRO330 4.0 32.1 1.0
CA A:LYS331 4.0 32.4 1.0
C A:PRO330 4.0 28.3 1.0
CD A:LYS331 4.1 42.5 1.0
C A:GLU329 4.3 35.8 1.0
CA A:GLU329 4.5 33.1 1.0
CG A:GLU329 4.6 38.9 1.0
CE A:LYS331 4.7 46.4 1.0
CD A:GLU329 4.7 44.3 1.0
O A:ARG182 4.7 21.6 1.0

Chlorine binding site 5 out of 5 in 3rh5

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Chlorine binding site 5 out of 5 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl355

b:43.0
occ:1.00
 N A:HIS34 3.3 29.2 1.0
C A:ALA32 3.4 28.9 1.0
CB A:ALA32 3.5 32.0 1.0
CA A:ALA32 3.5 30.0 1.0
CB A:HIS34 3.6 31.7 1.0
N A:ILE33 3.6 27.2 1.0
N A:LYS35 3.6 27.8 1.0
O A:ALA32 3.7 29.4 1.0
CA A:HIS34 3.8 28.2 1.0
CD2 A:HIS34 4.0 27.3 1.0
CG A:HIS34 4.1 31.4 1.0
C A:HIS34 4.2 27.8 1.0
C A:ILE33 4.3 29.9 1.0
CG A:LYS35 4.3 32.5 1.0
CA A:ILE33 4.5 29.7 1.0
O A:HOH392 4.6 33.1 1.0
CB A:LYS35 4.6 27.4 1.0
CA A:LYS35 4.7 26.4 1.0
O6 D:DG1 4.9 30.1 1.0
N A:ALA32 5.0 29.3 1.0
CG2 A:ILE33 5.0 33.9 1.0

Reference:

N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson. Molecular Insights Into Dna Polymerase Deterrents For Ribonucleotide Insertion. J.Biol.Chem. V. 286 31650 2011.
ISSN: ISSN 0021-9258
PubMed: 21733843
DOI: 10.1074/JBC.M111.253401
Page generated: Sat Dec 12 10:07:04 2020

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