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Chlorine in PDB 3jpq: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene 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-Monobromo Methylene Triphosphate, PDB code: 3jpq was solved by V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodman, C.E.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.23 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.680, 80.180, 55.560, 90.00, 107.82, 90.00
R / Rfree (%) 19.3 / 23.4

Other elements in 3jpq:

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

Bromine (Br) 2 atoms
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-Monobromo Methylene Triphosphate (pdb code 3jpq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 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-Monobromo Methylene Triphosphate, PDB code: 3jpq:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3jpq

Go back to Chlorine Binding Sites List in 3jpq
Chlorine binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene 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-Monobromo Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:28.5
occ:1.00
 NH2 A:ARG299 3.0 28.4 1.0
OG1 A:THR297 3.2 21.0 1.0
ND2 A:ASN294 3.2 19.1 1.0
NE A:ARG299 3.3 27.5 1.0
O A:HOH595 3.4 39.2 1.0
O T:HOH452 3.5 42.9 1.0
CZ A:ARG299 3.6 28.5 1.0
OD1 A:ASN294 3.9 19.4 1.0
CB A:TYR296 4.0 16.2 1.0
CG A:ASN294 4.0 17.6 1.0
CG2 A:THR297 4.1 22.0 1.0
CD2 A:TYR296 4.2 16.9 1.0
CB A:THR297 4.2 19.7 1.0
O A:HOH439 4.3 41.9 1.0
CD A:ARG299 4.6 24.4 1.0
CG A:TYR296 4.6 17.2 1.0
N A:THR297 4.6 17.0 1.0
O A:HOH481 4.7 20.3 1.0
O A:HOH397 4.8 40.7 1.0
NH1 A:ARG299 4.9 30.0 1.0
O T:HOH437 4.9 43.9 1.0
O T:HOH156 5.0 33.0 1.0
C A:TYR296 5.0 15.8 1.0

Chlorine binding site 2 out of 3 in 3jpq

Go back to Chlorine Binding Sites List in 3jpq
Chlorine binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene 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-Monobromo Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:32.8
occ:1.00
 O A:HOH672 2.9 43.5 1.0
N A:HIS34 3.3 24.1 1.0
CB A:HIS34 3.4 26.1 1.0
CB A:ALA32 3.5 22.9 1.0
CA A:ALA32 3.5 23.4 1.0
C A:ALA32 3.5 23.8 1.0
N A:LYS35 3.7 21.2 1.0
CA A:HIS34 3.7 24.6 1.0
O A:ALA32 3.8 23.9 1.0
N A:ILE33 3.9 24.4 1.0
CD2 A:HIS34 3.9 28.7 1.0
CG A:HIS34 3.9 29.2 1.0
C A:HIS34 4.2 23.1 1.0
C A:ILE33 4.3 23.3 1.0
CG A:LYS35 4.4 21.5 1.0
O A:HOH505 4.5 32.5 1.0
CB A:LYS35 4.6 19.9 1.0
CA A:ILE33 4.6 24.7 1.0
CA A:LYS35 4.7 19.6 1.0
CG2 A:ILE33 4.9 26.4 1.0
O6 D:DG1 4.9 29.9 1.0
N A:ALA32 4.9 21.6 1.0

Chlorine binding site 3 out of 3 in 3jpq

Go back to Chlorine Binding Sites List in 3jpq
Chlorine binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene 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-Monobromo Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:23.4
occ:1.00
 O A:HOH470 3.1 18.0 1.0
N A:CYS267 3.2 15.5 1.0
N A:TYR266 3.4 16.9 1.0
C A:GLN264 3.5 18.5 1.0
CA A:GLN264 3.5 17.9 1.0
CB A:TYR266 3.6 19.2 1.0
O A:GLN264 3.7 18.3 1.0
CG1 A:VAL313 3.7 16.5 1.0
CA A:TYR266 3.8 16.5 1.0
SG A:CYS267 3.8 15.4 1.0
O A:HOH464 3.8 35.1 1.0
O A:ASP263 3.9 21.3 1.0
CB A:VAL313 3.9 18.6 1.0
N A:TYR265 3.9 17.7 1.0
C A:TYR266 4.0 16.6 1.0
CB A:CYS267 4.0 15.9 1.0
CA A:CYS267 4.2 15.6 1.0
CD2 A:TYR266 4.3 23.7 1.0
C A:TYR265 4.3 17.3 1.0
CG A:TYR266 4.4 22.0 1.0
CB A:GLN264 4.4 19.1 1.0
O A:TYR296 4.5 15.6 1.0
N A:GLN264 4.5 18.4 1.0
O A:VAL313 4.5 21.9 1.0
C A:ASP263 4.6 19.2 1.0
CA A:TYR265 4.7 18.4 1.0
CG2 A:VAL313 4.7 16.6 1.0

Reference:

V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.Mckenna. Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Fri Jul 11 06:40:29 2025

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