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Chlorine in PDB 2pxi: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate, PDB code: 2pxi was solved by C.E.Mckenna, V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.09 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.600, 80.200, 55.400, 90.00, 107.80, 90.00
R / Rfree (%) 20.6 / 27

Other elements in 2pxi:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate (pdb code 2pxi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate, PDB code: 2pxi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2pxi

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Chlorine binding site 1 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:37.6
occ:1.00
 O A:HOH456 3.0 28.4 1.0
N A:CYS267 3.3 24.3 1.0
CG1 A:VAL313 3.5 24.5 1.0
CA A:GLN264 3.6 28.4 1.0
C A:GLN264 3.6 28.0 1.0
CB A:TYR266 3.7 28.9 1.0
N A:TYR266 3.7 26.3 1.0
CB A:VAL313 3.7 27.5 1.0
SG A:CYS267 3.8 24.8 1.0
O A:ASP263 3.8 28.8 1.0
O A:GLN264 3.9 27.8 1.0
CA A:TYR266 4.0 26.6 1.0
CB A:CYS267 4.0 25.5 1.0
C A:TYR266 4.1 25.5 1.0
N A:TYR265 4.1 27.4 1.0
CA A:CYS267 4.3 23.7 1.0
O A:TYR296 4.3 28.2 1.0
CD2 A:TYR266 4.4 33.0 1.0
O A:VAL313 4.5 28.5 1.0
CB A:GLN264 4.5 28.6 1.0
C A:TYR265 4.5 27.0 1.0
CG A:TYR266 4.5 31.5 1.0
N A:GLN264 4.5 28.9 1.0
CG2 A:VAL313 4.6 25.5 1.0
C A:ASP263 4.6 29.3 1.0
C A:VAL313 4.9 28.2 1.0
CA A:TYR265 4.9 27.5 1.0
CA A:VAL313 4.9 29.1 1.0
CG A:GLN264 5.0 29.2 1.0

Chlorine binding site 2 out of 5 in 2pxi

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Chlorine binding site 2 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:44.0
occ:1.00
 N A:HIS34 3.2 30.2 1.0
C A:ALA32 3.3 27.0 1.0
CB A:ALA32 3.3 24.9 1.0
CA A:ALA32 3.4 27.9 1.0
CB A:HIS34 3.4 33.2 1.0
N A:LYS35 3.4 30.7 1.0
O A:ALA32 3.6 26.4 1.0
CA A:HIS34 3.7 33.2 1.0
N A:ILE33 3.7 26.9 1.0
CD2 A:HIS34 3.9 37.4 1.0
CG A:HIS34 3.9 37.8 1.0
CG A:LYS35 4.0 29.6 1.0
C A:HIS34 4.0 33.0 1.0
C A:ILE33 4.2 29.4 1.0
O A:HOH372 4.4 34.3 1.0
CB A:LYS35 4.4 30.4 1.0
CA A:LYS35 4.5 28.6 1.0
CA A:ILE33 4.5 29.4 1.0
N A:ALA32 4.8 26.7 1.0
CG2 A:ILE33 4.9 32.0 1.0
O6 D:DG1 5.0 34.5 1.0
CD A:LYS35 5.0 32.5 1.0

Chlorine binding site 3 out of 5 in 2pxi

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Chlorine binding site 3 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:52.2
occ:1.00
 N A:LEU82 3.3 33.0 1.0
NH2 A:ARG89 3.5 46.6 1.0
O A:HOH480 3.6 50.4 1.0
CA A:LYS81 3.7 34.6 1.0
NH1 A:ARG89 3.7 48.0 1.0
CB A:LYS81 3.8 38.3 1.0
C A:LYS81 3.9 33.4 1.0
OE2 A:GLU86 3.9 52.6 1.0
CZ A:ARG89 4.1 46.1 1.0
CD1 A:LEU85 4.1 31.9 1.0
O A:LEU82 4.1 32.7 1.0
CB A:LEU82 4.1 33.7 1.0
CA A:LEU82 4.2 34.2 1.0
CB A:LEU85 4.2 32.7 1.0
C A:LEU82 4.6 33.5 1.0
CE1 A:PHE76 4.7 31.9 1.0
CG A:LEU85 4.8 32.8 1.0
O A:GLY80 4.8 34.5 1.0
CD1 A:PHE76 4.9 31.2 1.0
CD A:GLU86 5.0 52.7 1.0
N A:LYS81 5.0 33.9 1.0

Chlorine binding site 4 out of 5 in 2pxi

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Chlorine binding site 4 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:35.1
occ:1.00
 NH2 A:ARG299 2.8 18.4 0.5
ND2 A:ASN294 3.1 22.3 1.0
OG1 A:THR297 3.3 31.8 1.0
CZ A:ARG299 3.4 21.5 0.5
O A:HOH416 3.4 48.7 1.0
NE A:ARG299 3.6 21.6 0.5
NH1 A:ARG299 3.9 35.7 0.5
CZ A:ARG299 3.9 35.3 0.5
OD1 A:ASN294 3.9 24.5 1.0
CG A:ASN294 4.0 25.3 1.0
CB A:TYR296 4.0 28.5 1.0
CD2 A:TYR296 4.1 30.5 1.0
NH2 A:ARG299 4.2 34.7 0.5
NE A:ARG299 4.3 33.6 0.5
NH1 A:ARG299 4.4 20.6 0.5
CG A:TYR296 4.5 30.3 1.0
CB A:THR297 4.5 32.2 1.0
O A:HOH415 4.6 24.9 1.0
O A:HOH561 4.6 46.0 1.0
CD A:ARG299 4.7 33.8 0.5
N A:THR297 4.7 29.0 1.0
CD A:ARG299 4.7 25.7 0.5
CG2 A:THR297 4.7 32.7 1.0

Chlorine binding site 5 out of 5 in 2pxi

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Chlorine binding site 5 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl347

b:44.1
occ:1.00
 N A:LYS331 2.9 28.1 1.0
CD A:PRO330 3.1 24.7 1.0
CB A:PRO330 3.4 24.5 1.0
N A:PRO330 3.4 25.4 1.0
CB A:LYS331 3.5 32.7 1.0
CG A:LYS331 3.6 36.3 1.0
CG A:PRO330 3.7 25.8 1.0
CA A:PRO330 3.7 25.7 1.0
C A:PRO330 3.8 26.0 1.0
CA A:LYS331 3.8 30.1 1.0
CB A:GLU329 3.9 33.2 1.0
C A:GLU329 4.1 26.3 1.0
CD A:LYS331 4.1 38.5 1.0
OE1 A:GLU329 4.2 45.5 1.0
O A:ARG182 4.3 23.1 1.0
CA A:GLU329 4.5 29.0 1.0
CG A:GLU329 4.8 38.5 1.0
O A:GLU329 4.8 25.1 1.0
O A:PRO330 4.9 23.6 1.0
CE A:LYS331 5.0 41.8 1.0

Reference:

C.E.Mckenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, S.H.Wilson. (R)-Beta,Gamma-Fluoromethylene-Dgtp-Dna Ternary Complex with Dna Polymerase Beta. J.Am.Chem.Soc. V. 129 15412 2007.
ISSN: ISSN 0002-7863
PubMed: 18031037
DOI: 10.1021/JA072127V
Page generated: Sat Dec 12 09:15:56 2020

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