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Chlorine in PDB 3rh4: Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

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

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

Protein crystallography data

The structure of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh4 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) 22.59 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.170, 79.790, 55.000, 90.00, 107.95, 90.00
R / Rfree (%) 17.5 / 24

Other elements in 3rh4:

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

Manganese (Mn) 8 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) (pdb code 3rh4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3rh4

Go back to Chlorine Binding Sites List in 3rh4
Chlorine binding site 1 out of 6 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl353

b:38.2
occ:1.00
 OG1 A:THR297 3.2 23.3 1.0
ND2 A:ASN294 3.3 22.7 1.0
O A:HOH538 3.6 31.4 1.0
CG2 A:THR297 3.8 24.9 1.0
CB A:TYR296 4.0 22.1 1.0
OD1 A:ASN294 4.0 22.8 1.0
CG A:ASN294 4.1 20.5 1.0
NE A:ARG299 4.1 33.5 1.0
CB A:THR297 4.1 23.9 1.0
CZ A:ARG299 4.2 37.1 1.0
CD2 A:TYR296 4.3 21.1 1.0
NH2 A:ARG299 4.4 34.9 1.0
CG A:TYR296 4.5 20.2 1.0
CD A:ARG299 4.6 28.9 1.0
N A:THR297 4.7 21.4 1.0
NH1 A:ARG299 4.7 35.5 1.0
O A:HOH662 4.8 38.9 1.0
O A:HOH471 4.8 27.4 1.0
O T:HOH302 4.9 38.2 1.0

Chlorine binding site 2 out of 6 in 3rh4

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Chlorine binding site 2 out of 6 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl354

b:43.2
occ:1.00
 N A:HIS34 3.3 23.2 1.0
CB A:ALA32 3.3 22.7 1.0
C A:ALA32 3.4 28.8 1.0
CA A:ALA32 3.4 24.9 1.0
CB A:HIS34 3.5 24.6 1.0
N A:ILE33 3.6 22.0 1.0
N A:LYS35 3.7 23.5 1.0
CA A:HIS34 3.8 22.7 1.0
CD2 A:HIS34 3.9 21.3 1.0
O A:ALA32 3.9 25.6 1.0
CG A:HIS34 4.0 24.0 1.0
C A:HIS34 4.2 23.3 1.0
CG A:LYS35 4.3 24.1 1.0
C A:ILE33 4.3 30.3 1.0
CA A:ILE33 4.5 26.2 1.0
CB A:LYS35 4.6 23.0 1.0
O T:HOH371 4.7 44.6 1.0
O A:HOH665 4.7 32.2 1.0
CA A:LYS35 4.8 15.2 1.0
CG2 A:ILE33 4.8 36.4 1.0
N A:ALA32 4.9 27.4 1.0
O6 D:DG1 4.9 22.4 1.0

Chlorine binding site 3 out of 6 in 3rh4

Go back to Chlorine Binding Sites List in 3rh4
Chlorine binding site 3 out of 6 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl355

b:47.0
occ:1.00
 NH1 A:ARG89 3.2 56.9 1.0
N A:LEU82 3.3 21.6 1.0
OE2 A:GLU86 3.4 49.0 1.0
O A:HOH394 3.5 41.4 1.0
CA A:LYS81 3.8 26.0 1.0
C A:LYS81 4.0 25.2 1.0
CZ A:ARG89 4.1 54.2 1.0
O A:LEU82 4.1 26.0 1.0
CB A:LEU82 4.2 24.3 1.0
CA A:LEU82 4.2 23.6 1.0
CB A:LYS81 4.2 30.0 1.0
CB A:LEU85 4.3 29.9 1.0
CD1 A:LEU85 4.4 27.7 1.0
NH2 A:ARG89 4.4 42.9 1.0
CD A:GLU86 4.5 55.5 1.0
C A:LEU82 4.6 26.9 1.0
O A:GLY80 4.6 31.0 1.0
CG A:GLU86 4.8 36.7 1.0
CG A:LYS81 4.9 43.3 1.0
CG A:LEU85 5.0 32.6 1.0

Chlorine binding site 4 out of 6 in 3rh4

Go back to Chlorine Binding Sites List in 3rh4
Chlorine binding site 4 out of 6 in the Dna Polymerase Beta 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 4 of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl356

b:47.4
occ:1.00
 N A:LYS331 2.9 25.4 1.0
CG A:LYS331 3.3 38.9 1.0
CB A:LYS331 3.4 32.4 1.0
N A:PRO330 3.5 28.0 1.0
CD A:PRO330 3.6 30.9 1.0
CB A:PRO330 3.6 20.4 1.0
CA A:LYS331 3.7 25.1 1.0
CB A:GLU329 3.8 34.7 1.0
C A:PRO330 3.8 22.6 1.0
CA A:PRO330 3.9 25.2 1.0
CG A:PRO330 3.9 21.2 1.0
CD A:LYS331 4.1 42.1 1.0
C A:GLU329 4.1 30.3 1.0
OE2 A:GLU329 4.3 52.3 1.0
CA A:GLU329 4.5 32.2 1.0
CE A:LYS331 4.5 60.2 1.0
O A:ARG182 4.5 17.7 1.0
CG A:GLU329 4.7 40.2 1.0
O A:GLU329 4.8 24.8 1.0
C A:LYS331 4.9 31.7 1.0
O A:PRO330 5.0 24.1 1.0
CD A:GLU329 5.0 45.3 1.0

Chlorine binding site 5 out of 6 in 3rh4

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Chlorine binding site 5 out of 6 in the Dna Polymerase Beta 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 5 of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl357

b:41.9
occ:1.00
 OE1 A:GLN159 2.6 29.6 1.0
N A:VAL177 3.2 21.8 1.0
O A:HOH493 3.2 27.8 1.0
CD A:GLN159 3.6 24.7 1.0
CG2 A:VAL177 3.7 23.9 1.0
CA A:THR176 3.9 23.3 1.0
CB A:VAL177 3.9 21.7 1.0
C A:THR176 4.0 31.7 1.0
O A:HOH345 4.0 42.0 1.0
CA A:VAL177 4.1 22.5 1.0
CG A:GLN159 4.2 21.4 1.0
O A:ALA175 4.3 23.8 1.0
CD2 A:LEU163 4.4 33.7 1.0
CG2 A:THR176 4.4 21.9 1.0
O A:VAL177 4.4 17.3 1.0
O A:HOH583 4.6 34.1 1.0
NE2 A:GLN159 4.7 22.6 1.0
C A:VAL177 4.7 21.6 1.0
CE2 A:PHE181 4.8 26.3 1.0
CB A:THR176 4.8 30.1 1.0
CD1 A:LEU163 4.8 27.1 1.0
N A:THR176 4.9 21.7 1.0

Chlorine binding site 6 out of 6 in 3rh4

Go back to Chlorine Binding Sites List in 3rh4
Chlorine binding site 6 out of 6 in the Dna Polymerase Beta 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 6 of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl358

b:61.4
occ:1.00
 O A:HOH633 2.9 42.2 1.0
NZ A:LYS84 3.3 39.0 1.0
O A:HOH567 3.8 50.3 1.0
CG A:LYS84 4.1 31.2 1.0
CE A:LYS84 4.1 37.8 1.0
CG1 A:ILE88 4.2 30.9 1.0
CZ A:PHE25 4.2 26.3 1.0
CD1 A:ILE88 4.2 27.3 1.0
O A:HOH503 4.3 30.6 1.0
NZ A:LYS87 4.3 44.7 1.0
O A:HOH417 4.3 51.4 1.0
CE1 A:PHE25 4.4 29.6 1.0
O A:HOH623 4.4 49.1 1.0
CE A:LYS87 4.5 49.9 1.0
CD A:LYS87 4.5 55.1 1.0
CD A:LYS84 4.6 31.4 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: Sun Jul 21 03:40:34 2024

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