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Chlorine in PDB 3rh6: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

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

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

Protein crystallography data

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6 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) 20.77 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.060, 79.810, 55.060, 90.00, 107.68, 90.00
R / Rfree (%) 19.5 / 26.6

Other elements in 3rh6:

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

Manganese (Mn) 6 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 Ribonucleotide (Rctp) (pdb code 3rh6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3rh6

Go back to Chlorine Binding Sites List in 3rh6
Chlorine binding site 1 out of 3 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl348

b:44.4
occ:1.00
 OG1 A:THR297 3.1 29.7 1.0
ND2 A:ASN294 3.3 27.0 1.0
CG2 A:THR297 3.7 36.1 1.0
OD1 A:ASN294 3.9 26.7 1.0
CB A:THR297 4.0 35.2 1.0
CG A:ASN294 4.0 21.4 1.0
CZ A:ARG299 4.1 43.5 1.0
CB A:TYR296 4.1 30.3 1.0
NE A:ARG299 4.2 33.3 1.0
NH1 A:ARG299 4.2 45.8 1.0
CD2 A:TYR296 4.4 33.3 1.0
CD A:ARG299 4.5 32.5 1.0
NH2 A:ARG299 4.5 42.9 1.0
O A:HOH594 4.7 47.7 1.0
O A:HOH373 4.7 34.9 1.0
N A:THR297 4.7 27.4 1.0
CG A:TYR296 4.7 28.5 1.0
O T:HOH191 4.9 35.2 1.0
CA A:THR297 5.0 28.4 1.0

Chlorine binding site 2 out of 3 in 3rh6

Go back to Chlorine Binding Sites List in 3rh6
Chlorine binding site 2 out of 3 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl349

b:43.5
occ:1.00
 N A:HIS34 2.9 24.9 1.0
CB A:HIS34 3.1 31.5 1.0
C A:ALA32 3.3 25.4 1.0
CD2 A:HIS34 3.4 37.7 1.0
CA A:HIS34 3.5 29.8 1.0
N A:LYS35 3.5 22.1 1.0
N A:ILE33 3.5 22.2 1.0
CB A:ALA32 3.5 32.6 1.0
CA A:ALA32 3.6 33.7 1.0
CG A:HIS34 3.6 35.1 1.0
O A:ALA32 3.7 30.0 1.0
C A:HIS34 4.0 26.6 1.0
C A:ILE33 4.0 31.1 1.0
O A:HOH398 4.2 37.4 1.0
CA A:ILE33 4.3 29.7 1.0
CB A:LYS35 4.6 26.6 1.0
CA A:LYS35 4.7 19.3 1.0
CG2 A:ILE33 4.7 40.8 1.0
CG A:LYS35 4.7 25.3 1.0
NE2 A:HIS34 4.8 41.0 1.0
O6 D:DG1 4.8 26.3 1.0
ND1 A:HIS34 4.9 36.2 1.0

Chlorine binding site 3 out of 3 in 3rh6

Go back to Chlorine Binding Sites List in 3rh6
Chlorine binding site 3 out of 3 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl351

b:50.5
occ:1.00
 N A:LEU82 3.3 28.4 1.0
NH1 A:ARG89 3.3 43.6 1.0
O A:HOH590 3.3 44.1 1.0
NH2 A:ARG89 3.6 57.0 1.0
OE2 A:GLU86 3.7 48.7 1.0
CA A:LYS81 3.7 33.0 1.0
CZ A:ARG89 3.9 51.3 1.0
C A:LYS81 3.9 30.8 1.0
CD1 A:LEU85 4.0 41.1 1.0
CB A:LYS81 4.0 37.4 1.0
CB A:LEU85 4.1 33.6 1.0
O A:LEU82 4.2 32.3 1.0
CA A:LEU82 4.3 32.9 1.0
CB A:LEU82 4.3 33.0 1.0
CD A:GLU86 4.6 52.5 1.0
C A:LEU82 4.6 33.5 1.0
CG A:LEU85 4.7 37.0 1.0
O A:GLY80 4.8 32.1 1.0
CG A:GLU86 4.8 38.2 1.0
N A:LYS81 5.0 26.9 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: Fri Jul 11 09:50:44 2025

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